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A B C D E F G H I K L M N O P Q R S T U V W X Y Z

## A

A2Xml - Class in org.metaqtl.main
A2Xml() - Constructor for class org.metaqtl.main.A2Xml
absolute() - Method in interface org.metaqtl.bio.util.ILGroupPosition
absolute - Variable in class org.metaqtl.bio.util.LGroupPosition
absolute() - Method in class org.metaqtl.bio.util.LGroupPosition
adapt(Chromosome[]) - Static method in class org.metaqtl.adapter.MetaQtlAnalysisAdapter
adapt(EMResult) - Static method in class org.metaqtl.adapter.QtlAdapter
  From a result of a EM clustering returns the mixture components as an array of Qtl.
adapt(MetaQtlData) - Static method in class org.metaqtl.adapter.QtlPartitionAdapter
  Adapt the given `MetaQtlData` into a `QtlPartition` and returns it.
adapt(MetaQtlAnalysis, String, String, int) - Static method in class org.metaqtl.adapter.QtlPartitionAdapter
  Adapt the `MetaQtlAnalysis` `analysis` for a given value of the number of clusters `k` and a given trait name `code`.
adapt(MetaQtlResult, Qtl[], int) - Static method in class org.metaqtl.adapter.QtlPartitionAdapter
addAllele(IBioAllele) - Method in class org.metaqtl.bio.entity.AlleleContainer
addAllele(IBioAllele) - Method in interface org.metaqtl.bio.IBioLocus
addAllMap(IBioGenome[]) - Method in class org.metaqtl.MapCluster
addBooleanOption(char, String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a boolean option.
addBooleanOption(String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a boolean option.
addChild(TreeNode) - Method in class org.metaqtl.TreeNode
  Add a child to the node.
addChromosome(IBioLGroup, IBioCross, int, int, boolean, boolean) - Method in class org.metaqtl.ChromCluster
  Add a chromosome to the cluster
addChromosome(IBioLGroup, IBioCross, int, int, boolean, boolean) - Method in class org.metaqtl.MapCluster
  Add a chromosome to the map cluster framework.
addDoubleOption(char, String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a double option.
addDoubleOption(String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a double option.
addEdge(Chromosome, Chromosome, CMarkerSequence) - Method in class org.metaqtl.ChromCluster.ClusterGraph
addEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.BioEntityContainer
addGroup(IBioLGroup) - Method in class org.metaqtl.bio.entity.GroupContainer
addGroup(IBioLGroup) - Method in interface org.metaqtl.bio.IBioGenome
addIndividual(IBioIndividual) - Method in class org.metaqtl.bio.entity.IndividualContainer
addIndividual(IBioIndividual) - Method in interface org.metaqtl.bio.IBioPopulation
addIntegerOption(char, String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding an integer option.
addIntegerOption(String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding an integer option.
additive - Variable in class org.metaqtl.Qtl.QTLStats
  The additive effect of the QTL.
addLocus(IBioLocus) - Method in class org.metaqtl.bio.entity.LocusContainer
addLocus(IBioLocus) - Method in interface org.metaqtl.bio.IBioLGroup
addLongOption(char, String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a long integer option.
addLongOption(String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a long integer option.
addMap(IBioGenome, boolean) - Method in class org.metaqtl.MapCluster
  Add a map to the cluster.
addOption(CmdLineParser.Option) - Method in class org.metaqtl.main.CmdLineParser
  Add the specified Option to the list of accepted options
addQtl(Graphics2D, QtlUnit) - Method in class org.metaqtl.graph.QtlLayerBuffer
  Try to add a qtl unit to the configuration.
addStringOption(char, String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a string option.
addStringOption(String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a string option.
addTerm(String, String) - Method in class org.metaqtl.MetaDico
adjTable - Variable in class org.metaqtl.ChromCluster.ClusterGraph
AIC - Static variable in class org.metaqtl.EMCriteria
aic - Variable in class org.metaqtl.EMCriteria
AIC3 - Static variable in class org.metaqtl.EMCriteria
aic3 - Variable in class org.metaqtl.EMCriteria
AIC3_NAME - Static variable in class org.metaqtl.EMCriteria
AIC_NAME - Static variable in class org.metaqtl.EMCriteria
AICc - Static variable in class org.metaqtl.EMCriteria
aicc - Variable in class org.metaqtl.EMCriteria
AICc_NAME - Static variable in class org.metaqtl.EMCriteria
ALIGN_FIRST_COMMON - Static variable in class org.metaqtl.graph.ChromLayer
ALIGN_FIRST_MARKER - Static variable in class org.metaqtl.graph.ChromLayer
alignChromLayers(ChromLayer, ChromLayer, int) - Static method in class org.metaqtl.graph.ChromLayer
ALLELE - Static variable in interface org.metaqtl.bio.IBioEntityTypes
  The integer code for Allele entity
AlleleContainer - Class in org.metaqtl.bio.entity
  Class Description Here
AlleleContainer() - Constructor for class org.metaqtl.bio.entity.AlleleContainer
AlleleContainer(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.AlleleContainer
alleles() - Method in class org.metaqtl.bio.entity.AlleleContainer
alleles() - Method in interface org.metaqtl.bio.IBioLocus
AnchoredElement - Class in org.metaqtl.graph
AnchoredElement() - Constructor for class org.metaqtl.graph.AnchoredElement
areMarkersAroundQTL(int, int, int) - Method in class org.metaqtl.Chromosome
  Returns true if the QTL position is inside the marker interval which markers indices are `mrkIdxL` and `mrkIdxR`.
attach(Object) - Method in class org.metaqtl.graph.ChromLayer
attach(Object) - Method in class org.metaqtl.graph.Layer
  Attach the given `object` to the layer.
attach(Object) - Method in class org.metaqtl.graph.QtlLayer
attach(Object) - Method in class org.metaqtl.graph.QtlPartitionLayer
attach(Object) - Method in class org.metaqtl.graph.QtlTreeLayer
attachQtl(Qtl[]) - Method in class org.metaqtl.Chromosome
attachQTL(IBioLocus[]) - Method in class org.metaqtl.Chromosome
  Add
AWE - Static variable in class org.metaqtl.EMCriteria
awe - Variable in class org.metaqtl.EMCriteria
AWE_NAME - Static variable in class org.metaqtl.EMCriteria

## B

BACKGROUND_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
  The color of the backgroud.
base - Static variable in class org.metaqtl.graph.PaletteColor
BC - Static variable in interface org.metaqtl.bio.IBioCrossTypes
beta(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Returns the beta function I(a,b)
betacf(double, double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Used by betai : Evaluates continued fraction for incomplete beta function by modified Lentz's method.
betai(double, double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Returns the incomplete beta function Ix(a,b)
BIC - Static variable in class org.metaqtl.EMCriteria
bic - Variable in class org.metaqtl.EMCriteria
BIC_NAME - Static variable in class org.metaqtl.EMCriteria
BioCrossTypes - Class in org.metaqtl.bio.util
BioCrossTypes() - Constructor for class org.metaqtl.bio.util.BioCrossTypes
BioEntity - Class in org.metaqtl.bio.entity
  Class Description Here
BioEntity() - Constructor for class org.metaqtl.bio.entity.BioEntity
BioEntity(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.BioEntity
BioEntityAdapter - Class in org.metaqtl.bio.entity.adapter
  Class Description Here
BioEntityAdapter() - Constructor for class org.metaqtl.bio.entity.adapter.BioEntityAdapter
BioEntityBean - Class in org.metaqtl.bio.entity.bean
  Class Description Here
BioEntityBean() - Constructor for class org.metaqtl.bio.entity.bean.BioEntityBean
BioEntityCollection - Class in org.metaqtl.bio.entity
  Class Description Here
BioEntityCollection() - Constructor for class org.metaqtl.bio.entity.BioEntityCollection
BioEntityCollection(int) - Constructor for class org.metaqtl.bio.entity.BioEntityCollection
BioEntityCollectionAdapter - Class in org.metaqtl.bio.entity.adapter
  Class Description Here
BioEntityCollectionAdapter() - Constructor for class org.metaqtl.bio.entity.adapter.BioEntityCollectionAdapter
BioEntityCollectionBean - Class in org.metaqtl.bio.entity.bean
  Class Description Here
BioEntityCollectionBean() - Constructor for class org.metaqtl.bio.entity.bean.BioEntityCollectionBean
BioEntityContainer - Class in org.metaqtl.bio.entity
  Class Description Here
BioEntityContainer() - Constructor for class org.metaqtl.bio.entity.BioEntityContainer
BioEntityContainer(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.BioEntityContainer
BioEntityFactory - Class in org.metaqtl.bio.entity.factory
  Class Description Here
BioEntityFactory() - Constructor for class org.metaqtl.bio.entity.factory.BioEntityFactory
BioEntityNameComparator - Class in org.metaqtl.bio.util
  Class Description Here
BioLocusTypes - Class in org.metaqtl.bio.util
BioLocusTypes() - Constructor for class org.metaqtl.bio.util.BioLocusTypes
BioUtilities - Class in org.metaqtl.bio.util
  General comments must be added here.
BioUtilities() - Constructor for class org.metaqtl.bio.util.BioUtilities
BOX_HEIGHT - Static variable in class org.metaqtl.graph.GraphFactory
BOX_WIDTH - Static variable in class org.metaqtl.graph.GraphFactory
build(Graphics2D) - Method in class org.metaqtl.graph.ChromLayer
build(Graphics2D) - Method in class org.metaqtl.graph.Layer
  Build the layer.
build(Graphics2D) - Method in class org.metaqtl.graph.QtlLayer
build(Graphics2D) - Method in class org.metaqtl.graph.QtlPartitionLayer
build(Graphics2D) - Method in class org.metaqtl.graph.QtlTreeLayer
buildMetaChrom(ChromCluster) - Method in class org.metaqtl.algo.MetaMapAlgorithm
  For a cluster of chromosomes `cluster` this method builds the consensus chromosome using a Weighted Least Square strategy and returns the result as a `MetaChrom` object.
buildQtlTree(MetaQtlData) - Method in class org.metaqtl.algo.QtlTreeAlgorithm
  For the given data points this method build the tree which represents the hierarchical clustering.
buildShape(Graphics2D, Object) - Method in class org.metaqtl.graph.ChromShape
buildShape(Graphics2D, Object) - Method in class org.metaqtl.graph.GraphShape
buildShape(Graphics2D, Object) - Method in class org.metaqtl.graph.QtlShape
  This methods create a new QtlShape from the given graphics context.

## C

C - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
c1 - Variable in class org.metaqtl.Qtl
  The recombination rate between the QTL position and the left flanking marker.
c2 - Variable in class org.metaqtl.Qtl
  The recombination rate between the QTL position and the right flanking marker.
C_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
canAddMoreQtl(double) - Method in class org.metaqtl.graph.QtlLayerBuffer
  Retruns true if more Qtl can be added to the configuration, false otherwise.
card - Variable in class org.metaqtl.TreeNode
  The number of sequences in the cluster
cartoFunction - Static variable in interface org.metaqtl.bio.entity.IGeneticMapProperties
cartoFunctionHaldane - Static variable in interface org.metaqtl.bio.entity.IGeneticMapProperties
cartoFunctionKey - Static variable in interface org.metaqtl.bio.entity.IGeneticMapProperties
cartoFunctionKosambi - Static variable in interface org.metaqtl.bio.entity.IGeneticMapProperties
ccov - Variable in class org.metaqtl.EMResult
  The complete information (just for means).
CENTROID_METHOD - Static variable in class org.metaqtl.algo.HClustAlgorithm
  Centroid method
CentroidMethod(double[], double[]) - Static method in class org.metaqtl.algo.HClustAlgorithm
  This method performs a hierarchical clustering of the given data points using a centroid method based on the mahalanobis distance.
cg - Variable in class org.metaqtl.Chromosome
  The number of generations of the offspring population.
checkProjection(ChromCluster[]) - Method in class org.metaqtl.algo.QtlProjAlgorithm
chi2 - Variable in class org.metaqtl.MetaChrom
  The chi-square value of this chromosome.
chi2 - Variable in class org.metaqtl.MultiFitResult
  The chi-square of the model.
children - Variable in class org.metaqtl.bio.entity.bean.OntologyTermBean
  The children of the term.
children - Variable in class org.metaqtl.TreeNode
  Left and right children, or null
CHISQUARE - Static variable in interface org.metaqtl.IBioLGroupProperties
  The key for the chisquare value.
chrName - Variable in class org.metaqtl.algo.ClustAlgorithm
  The name of the chromosome to study.
chrom - Variable in class org.metaqtl.ChromCluster.ClusterEdge
CHROM_ALIGN_MODE - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_DISTANCE_SCALE - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_FLANKING_CEX - Static variable in class org.metaqtl.graph.MetaGraphPar
  The default cex parameter for flanking regions at the top and the end of the chromosome.
CHROM_NAME_FONT - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_NAME_HSPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_STROKE - Static variable in class org.metaqtl.graph.MetaGraphPar
  The stroke of the chromosome shape.
CHROM_STROKE_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
  The color of the stroke of the Chromosome shape.
CHROM_TICK_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
  The color of the marker ticks on the chromosome.
CHROM_TICK_STROKE - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_TICK_WIDTH_1 - Static variable in class org.metaqtl.graph.MetaGraphPar
  The width of the marker ticks.
CHROM_TICK_WIDTH_2 - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_TICK_WIDTH_3 - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
  The width of the chromosome.
ChromAxe - Class in org.metaqtl.graph
ChromAxe(double, double, double) - Constructor for class org.metaqtl.graph.ChromAxe
ChromCluster - Class in org.metaqtl
  A cluster of chromosomes which share the same name inside a `MapCluster` framwork.
ChromCluster() - Constructor for class org.metaqtl.ChromCluster
  Creates a new instance if ChromCluster.
ChromCluster.ClusterEdge - Class in org.metaqtl
ChromCluster.ClusterEdge(CMarkerSequence, Chromosome) - Constructor for class org.metaqtl.ChromCluster.ClusterEdge
ChromCluster.ClusterGraph - Class in org.metaqtl
ChromCluster.ClusterGraph(ChromCluster) - Constructor for class org.metaqtl.ChromCluster.ClusterGraph
ChromGraph - Class in org.metaqtl.graph
  A `ChromGraph` allows to link together a `Chromosome` and a `QtlPartition` in order to be depicted into a graphic.
ChromGraph() - Constructor for class org.metaqtl.graph.ChromGraph
ChromLayer - Class in org.metaqtl.graph
ChromLayer(double, double) - Constructor for class org.metaqtl.graph.ChromLayer
ChromLayer.CMrkTickPath - Class in org.metaqtl.graph
ChromLayer.CMrkTickPath() - Constructor for class org.metaqtl.graph.ChromLayer.CMrkTickPath
ChromLayer.CMrkTickPoint - Class in org.metaqtl.graph
ChromLayer.CMrkTickPoint() - Constructor for class org.metaqtl.graph.ChromLayer.CMrkTickPoint
chromNames - Variable in class org.metaqtl.MetaQtlAnalysis
  The names of the chromosomes.
chromNames - Variable in class org.metaqtl.MetaQtlModel
  The chromosomes.
Chromosome - Class in org.metaqtl
  On a Chromosome there are two types of locus : Marker QTL (Quantitative Trait Loci) inside a mapping context which is defined by both the mapping framework (function and unit) and the population cross design used to build this chromosome.
Chromosome() - Constructor for class org.metaqtl.Chromosome
chromosome - Variable in class org.metaqtl.graph.ChromGraph
  The chromosome to draw
ChromosomeAdapter - Class in org.metaqtl.adapter
  This class defines some usefull methods to adapt `Chromosome` objects into other kinds of objects or the inverse.
ChromosomeAdapter() - Constructor for class org.metaqtl.adapter.ChromosomeAdapter
chromosomes - Variable in class org.metaqtl.algo.ClustAlgorithm
  The chromosome on which the clustering is performed.
chromosomes - Variable in class org.metaqtl.MetaMap
  The meta chromosomes.
ChromShape - Class in org.metaqtl.graph
ChromShape() - Constructor for class org.metaqtl.graph.ChromShape
ci - Variable in class org.metaqtl.Qtl
  The QTL confidence interval.
ci2sd(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
ci_height - Variable in class org.metaqtl.graph.QtlShape
CI_MISS_IGNORE - Static variable in interface org.metaqtl.IMetaQtlConstants
  MSD Mode : ignore QTL with missing standard deviation.
CI_MISS_IMPUTATION - Static variable in interface org.metaqtl.IMetaQtlConstants
  MSD Mode : replace missing standard deviation by the mean of the observed ones.
CI_MODE_AVAILABLE - Static variable in interface org.metaqtl.IMetaQtlConstants
  SD Mode : use the available information to compute the standard deviation.
CI_MODE_LOD - Static variable in interface org.metaqtl.IMetaQtlConstants
  SD Mode : use only the confidence interval information if defined to compute the standard deviation.
CI_MODE_MAXIMAL - Static variable in interface org.metaqtl.IMetaQtlConstants
  SD Mode : compute the standard deviation using both lod support and rsquare information (if available) and then choose the maximal standard-deviation.
CI_MODE_RSQUARE - Static variable in interface org.metaqtl.IMetaQtlConstants
  SD Mode : use only the rsquare information if defined to compute the standard deviation.
CI_WIDTH - Static variable in class org.metaqtl.graph.QtlLayer
  The default width of the CI of the Qtl
ci_width - Variable in class org.metaqtl.graph.QtlShape
clog - Variable in class org.metaqtl.EMResult
  The complete loglikelihood.
close() - Method in class org.metaqtl.bio.util.TabulatedReader
  Closes the stream.
close() - Method in class org.metaqtl.bio.util.TabulatedWriter
ClustAlgorithm - Class in org.metaqtl.algo
ClustAlgorithm(IBioGenome, IBioOntology) - Constructor for class org.metaqtl.algo.ClustAlgorithm
ClustAlgorithm(IBioGenome, String, IBioOntology) - Constructor for class org.metaqtl.algo.ClustAlgorithm
cluster - Variable in class org.metaqtl.ChromCluster.ClusterGraph
clusterings - Variable in class org.metaqtl.MetaQtlResult
  The meta qtl clusterings.
clusters - Variable in class org.metaqtl.ChromCluster
  The list of the cluster members.
CMarkerSequence - Class in org.metaqtl
  A Common marker sequence between two ordered set of markers is a sub-set of at least two markers which order is the same between the two sets (may be reverse).
CMarkerSequence(int[][], int) - Constructor for class org.metaqtl.CMarkerSequence
  Initiates a new Common marker sequence from the tow arrays of common marker indices `mcidx[0..1][0..nmc-1]`.
CmdLineParser - Class in org.metaqtl.main
  Largely GNU-compatible command-line options parser.
CmdLineParser() - Constructor for class org.metaqtl.main.CmdLineParser
CmdLineParser.IllegalOptionValueException - Exception in org.metaqtl.main
  Thrown when an illegal or missing value is given by the user for an option that takes a value.
CmdLineParser.IllegalOptionValueException(CmdLineParser.Option, String) - Constructor for exception org.metaqtl.main.CmdLineParser.IllegalOptionValueException
CmdLineParser.NotFlagException - Exception in org.metaqtl.main
  Thrown when the parsed commandline contains multiple concatenated short options, such as -abcd, where one or more requires a value.
CmdLineParser.NotFlagException(String, char) - Constructor for exception org.metaqtl.main.CmdLineParser.NotFlagException
CmdLineParser.Option - Class in org.metaqtl.main
  Representation of a command-line option
CmdLineParser.Option(String, boolean) - Constructor for class org.metaqtl.main.CmdLineParser.Option
CmdLineParser.Option(char, String, boolean) - Constructor for class org.metaqtl.main.CmdLineParser.Option
CmdLineParser.Option.BooleanOption - Class in org.metaqtl.main
CmdLineParser.Option.BooleanOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.BooleanOption
CmdLineParser.Option.BooleanOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.BooleanOption
CmdLineParser.Option.DoubleOption - Class in org.metaqtl.main
  An option that expects a floating-point value
CmdLineParser.Option.DoubleOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.DoubleOption
CmdLineParser.Option.DoubleOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.DoubleOption
CmdLineParser.Option.IntegerOption - Class in org.metaqtl.main
  An option that expects an integer value
CmdLineParser.Option.IntegerOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.IntegerOption
CmdLineParser.Option.IntegerOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.IntegerOption
CmdLineParser.Option.LongOption - Class in org.metaqtl.main
  An option that expects a long integer value
CmdLineParser.Option.LongOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.LongOption
CmdLineParser.Option.LongOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.LongOption
CmdLineParser.Option.StringOption - Class in org.metaqtl.main
  An option that expects a string value
CmdLineParser.Option.StringOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.StringOption
CmdLineParser.Option.StringOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.StringOption
CmdLineParser.OptionException - Exception in org.metaqtl.main
  Base class for exceptions that may be thrown when options are parsed
CmdLineParser.OptionException(String) - Constructor for exception org.metaqtl.main.CmdLineParser.OptionException
CmdLineParser.UnknownOptionException - Exception in org.metaqtl.main
  Thrown when the parsed command-line contains an option that is not recognised.
CmdLineParser.UnknownOptionException(String) - Constructor for exception org.metaqtl.main.CmdLineParser.UnknownOptionException
CmdLineParser.UnknownOptionException(String, String) - Constructor for exception org.metaqtl.main.CmdLineParser.UnknownOptionException
CmdLineParser.UnknownSuboptionException - Exception in org.metaqtl.main
  Thrown when the parsed commandline contains multiple concatenated short options, such as -abcd, where one is unknown.
CmdLineParser.UnknownSuboptionException(String, char) - Constructor for exception org.metaqtl.main.CmdLineParser.UnknownSuboptionException
cms - Variable in class org.metaqtl.ChromCluster.ClusterEdge
CMSAlgorithm - Class in org.metaqtl.algo
  Use this class to find common marker sequences between two chromosomes.
CMSAlgorithm() - Constructor for class org.metaqtl.algo.CMSAlgorithm
COLLECTION - Static variable in interface org.metaqtl.bio.IBioEntityTypes
color2string(Color) - Static method in class org.metaqtl.graph.MetaGraphPar
COMMON_STROKE_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
compare(Object, Object) - Method in class org.metaqtl.bio.util.BioEntityNameComparator
compare(Object, Object) - Method in class org.metaqtl.bio.util.LocusPositionComparator
computeCOV(double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  Computes the variance-covariance matrix of the mixture component estimates.
computeCriteria() - Method in class org.metaqtl.EMResult
  This methos computes the following criteria : AIC AIC3 ICOMP MIR BIC AWE
computeDM(double[], double[], double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  Computes the matrix of derivatives of the update function.
computeQtlSD(int) - Method in class org.metaqtl.Chromosome
  According to the given standard deviation computation mode this method computes for each QTL the value of the standard deviation of the QTL position.
ConsMap - Class in org.metaqtl.main
ConsMap() - Constructor for class org.metaqtl.main.ConsMap
containsKey(String) - Method in class org.metaqtl.bio.util.TabulatedReader
  Returns true if the given string is a key of the tabulated file.
copy(EMResult, EMResult) - Static method in class org.metaqtl.EMResult
cov - Variable in class org.metaqtl.MultiFitResult
  The variance-covariance matrix of the parameter estimates.
criteria - Variable in class org.metaqtl.EMResult
  The model choice criteria.
cross - Variable in class org.metaqtl.Qtl
  The QTL cross design.
CROSS_SIZE - Static variable in interface org.metaqtl.IBioGenomeProperties
  The cross size key.
CROSS_TYPE - Static variable in interface org.metaqtl.IBioGenomeProperties
  The cross type key.
crossLayers - Variable in class org.metaqtl.graph.MetaGraph
CrossPopulation - Class in org.metaqtl.bio.entity
  Class Description Here
CrossPopulation() - Constructor for class org.metaqtl.bio.entity.CrossPopulation
CrossPopulation(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.CrossPopulation
CrossPopulation(String, IBioEntity, int) - Constructor for class org.metaqtl.bio.entity.CrossPopulation
crossToString(int, int) - Static method in class org.metaqtl.bio.util.BioCrossTypes
cs - Variable in class org.metaqtl.Chromosome
  The size of the offspring population.
css - Variable in class org.metaqtl.CMarkerSequence
  The sizes of the common sequences
ct - Variable in class org.metaqtl.Chromosome
  The type of the offspring population.

## D

d - Variable in class org.metaqtl.MetaChrom
  The absolute positions of markers in Morgan.
D - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
D_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
dataLayers - Variable in class org.metaqtl.graph.MetaGraph
dC - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
dD - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
dE - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
DEFAULT_HEIGHT - Static variable in class org.metaqtl.graph.MetaGraphPar
  The default height.
DEFAULT_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
  The default width.
DEFINITION - Static variable in interface org.metaqtl.bio.IOntologyTermProperties
  The definition property of a term in a ontology
dF - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
dfridr(NumericalUtilities.Function, double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Returns the derivative of a function func at a point x by Ridders' method of polynomial extrapolation.
dG - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
DH - Static variable in interface org.metaqtl.bio.IBioCrossTypes
disableLogger() - Method in class org.metaqtl.algo.MetaAlgorithm
dist - Variable in class org.metaqtl.TreeNode
  The distance between the node and its parent.
distance(double, int, int) - Static method in class org.metaqtl.util.MappingFunction
  Returns the distance from the recombination rate.
distanceUnitCM - Static variable in interface org.metaqtl.bio.entity.IGeneticMapProperties
distanceUnitKey - Static variable in interface org.metaqtl.bio.entity.IGeneticMapProperties
dm - Variable in class org.metaqtl.EMResult
  The matrix of convergence rate for the EM-Algorithm (just for means).
DMAX(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Returns the max between `a` and `b`
DO_SEM - Static variable in class org.metaqtl.algo.EMAlgorithm
  If true the best starting point is used to do Supplemental EM (SEM) in order to compute the DM Matrix..
doEM(double[], double[], int, EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  Apply the EM-Algorithm on the given data set where `x` is an array of observed value and `sd` an array of same size than `x` which stores the standard deviations of the observed values.
DOF - Static variable in interface org.metaqtl.IBioLGroupProperties
  The key for the number of degrees of freedom.
dof - Variable in class org.metaqtl.MetaChrom
  The number of degrees of freedom.
dof - Variable in class org.metaqtl.MultiFitResult
  The number of degrees of freedom.
dominance - Variable in class org.metaqtl.Qtl.QTLStats
  The dominance effect of the QTL.
doProjection(ChromCluster[]) - Method in class org.metaqtl.algo.QtlProjAlgorithm
doQtlClustering(MetaQtlData) - Method in class org.metaqtl.algo.QtlClustAlgorithm
  For a given data set `data` performs the clustering on each trait group and returns the results as an array of `MetaQtlResult` objects.
doTraitGroupClustering() - Method in class org.metaqtl.MetaQtlData
  According to the values of the QTLTrait.group attribute of the trait attribute of the qtls this methos clusterize the qtls in trait groups.
doTraitOntologyClustering(IBioOntology) - Method in class org.metaqtl.MetaQtlData
  According to the given trait ontology this methods clusterize the QTL in group in such a way that each group represents a trait term in the ontology.
draw(Graphics2D) - Method in class org.metaqtl.graph.ChromLayer
draw(Graphics2D) - Method in class org.metaqtl.graph.ChromShape
draw(Graphics2D) - Method in class org.metaqtl.graph.GraphShape
  Draws the shape.
draw(Graphics2D) - Method in class org.metaqtl.graph.Layer
  Draws the layer on the given `graph` context.
draw(Graphics2D, double, double) - Method in class org.metaqtl.graph.MetaGraph
draw(Graphics2D) - Method in class org.metaqtl.graph.QtlLayer
draw(Graphics2D) - Method in class org.metaqtl.graph.QtlPartitionLayer
draw(Graphics2D) - Method in class org.metaqtl.graph.QtlShape
draw(Graphics2D) - Method in class org.metaqtl.graph.QtlTreeLayer
DSWAP(double[], int, int) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Swaps elements i and j in a.
DUBIOUS_ORDER - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the marker dubious status.
DubiousLocusFactory - Class in org.metaqtl.factory
  A factory to read a list of dubious markers from a file.
DubiousLocusFactory() - Constructor for class org.metaqtl.factory.DubiousLocusFactory

## E

E - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
E_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
edist - Variable in class org.metaqtl.EMResult
  The euclidean distance between the current and the previous vector of parameters (mu + pi)
EM_CONTINUE - Static variable in class org.metaqtl.algo.EMAlgorithm
  The EM convergence status : continue
EM_ERR - Static variable in class org.metaqtl.algo.EMAlgorithm
  The EM convergence tolerance.
EM_FAILURE - Static variable in class org.metaqtl.algo.EMAlgorithm
  The EM convergence status : failure
EM_ITER_MAX - Static variable in class org.metaqtl.algo.EMAlgorithm
  The EM maximum number of iterations.
EM_MIN_DISTANCE - Static variable in class org.metaqtl.algo.EMAlgorithm
  The minimal mahalanobis distance between components.
EM_OK - Static variable in class org.metaqtl.algo.EMAlgorithm
  The EM convergence status : success
EM_START - Static variable in class org.metaqtl.algo.EMAlgorithm
  The number of replicates for a run of the EM-algorithm.
EMAlgorithm - Class in org.metaqtl.algo
  This class defines methods to perform the EM-algorithm for univariate mixture of gaussians with known variances.
EMAlgorithm() - Constructor for class org.metaqtl.algo.EMAlgorithm
EMCriteria - Class in org.metaqtl
EMCriteria() - Constructor for class org.metaqtl.EMCriteria
EMPTY_BIOALLELE_ARRAY - Static variable in interface org.metaqtl.bio.entity.IBioConstants
EMPTY_BIOENTITY_ARRAY - Static variable in interface org.metaqtl.bio.entity.IBioConstants
EMPTY_BIOLGROUP_ARRAY - Static variable in interface org.metaqtl.bio.entity.IBioConstants
EMPTY_BIOLOCUS_ARRAY - Static variable in interface org.metaqtl.bio.entity.IBioConstants
emRate(EMResult, double[], double[]) - Static method in class org.metaqtl.algo.EMAlgorithm
  Compute the euclidean distance between the new parameters and the old ones to obtain a simple approximation of the EM convergence rate.
EMResult - Class in org.metaqtl
EMResult() - Constructor for class org.metaqtl.EMResult
EMResult(int, int) - Constructor for class org.metaqtl.EMResult
EMResultFactory - Class in org.metaqtl.factory
EMResultFactory() - Constructor for class org.metaqtl.factory.EMResultFactory
entities - Variable in class org.metaqtl.bio.entity.bean.BioEntityCollectionBean
entities - Variable in class org.metaqtl.bio.entity.BioEntityContainer
entities() - Method in class org.metaqtl.bio.entity.BioEntityContainer
entityNumber() - Method in class org.metaqtl.bio.entity.BioEntityContainer
eStep(double[], double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  The Expectation step : it just consists in updating the Z matrix, i.e the cluster membership probabilities.
ESTIMATED - Static variable in interface org.metaqtl.bio.util.ILGroupPosition
EstimatedLocusPosition - Class in org.metaqtl.bio.util
  Class Description Here
EstimatedLocusPosition(double, double) - Constructor for class org.metaqtl.bio.util.EstimatedLocusPosition
extractLocus(IBioLocus[], int) - Static method in class org.metaqtl.bio.util.BioLocusTypes
  This returns extracts in the given array of loci the locus which type matches the given one.

## F

F - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
F_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
fisherVariance(double, int, int, int) - Static method in class org.metaqtl.util.OffspringManager
  Returns the inverse of the Fisher Information depending on the type of cross for a given recombination rate and a given population size.
fixCluster() - Method in class org.metaqtl.ChromCluster
  This methods frozes the index of the distinct markers over all the members of the cluster.
font2string(Font) - Static method in class org.metaqtl.graph.MetaGraphPar
formatDouble(double) - Static method in class org.metaqtl.bio.util.NumberFormat
frames - Variable in class org.metaqtl.CMarkerSequence
  The frame of the common marker sequences
from - Variable in class org.metaqtl.graph.QtlUnit
from - Variable in class org.metaqtl.Qtl.QTLSupport
  The position from the first marker to the left border of the IC.
fromEntity(IBioEntity, BioEntityBean) - Static method in class org.metaqtl.bio.entity.adapter.BioEntityAdapter
fromEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.adapter.BioEntityCollectionAdapter
fromEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.adapter.GeneticMapBeanAdapter
fromEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.adapter.LGroupBeanAdapter
fromEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.adapter.LocusBeanAdapter
fromEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.adapter.OntologyBeanAdapter
fromEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.adapter.OntologyTermBeanAdapter
fromEntity(IBioEntity) - Method in interface org.metaqtl.bio.IBioAdapter
  Convert the given compliant object to a bio entity object.
fromQTL(Qtl) - Static method in class org.metaqtl.adapter.QtlAdapter
  This method converts a `Qtl` into an object which class implements the `IBioLocus`interface.``
func(double) - Method in interface org.metaqtl.numrec.NumericalUtilities.Function
  Returns the value of the function in x.
funcd(double) - Method in interface org.metaqtl.numrec.NumericalUtilities.NRFunction
  Compute both the value and the derivate of the function in x.
function - Variable in class org.metaqtl.bio.entity.bean.OntologyBean
  The function of the ontology.

## G

G - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
G_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
GAMCOF - Static variable in class org.metaqtl.numrec.NumericalUtilities
gammln(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
gammp(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
gauss(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  This routine returns the value at x of the normal centered gaussian density.
gcf(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
gen - Static variable in class org.metaqtl.bio.util.BioCrossTypes
gen - Variable in class org.metaqtl.Qtl.QTLCross
  The number of generations.
generalHelp() - Static method in class org.metaqtl.main.MetaMain
generalUsage() - Static method in class org.metaqtl.main.MetaMain
generation - Variable in class org.metaqtl.bio.entity.Population
GeneticMap - Class in org.metaqtl.bio.entity
  Class Description Here
GeneticMap() - Constructor for class org.metaqtl.bio.entity.GeneticMap
GeneticMap(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.GeneticMap
GeneticMap(String) - Constructor for class org.metaqtl.bio.entity.GeneticMap
GeneticMapBean - Class in org.metaqtl.bio.entity.bean
  Class Description Here
GeneticMapBean() - Constructor for class org.metaqtl.bio.entity.bean.GeneticMapBean
GeneticMapBeanAdapter - Class in org.metaqtl.bio.entity.adapter
  Class Description Here
GeneticMapBeanAdapter() - Constructor for class org.metaqtl.bio.entity.adapter.GeneticMapBeanAdapter
GeneticMapProperties - Class in org.metaqtl.util
  General comments must be added here.
GeneticMapProperties() - Constructor for class org.metaqtl.util.GeneticMapProperties
GENOME - Static variable in interface org.metaqtl.bio.IBioEntityTypes
  The integer code for Genome entity
get(String) - Method in class org.metaqtl.bio.util.TabulatedReader
  Returns the value of the field which belongs to the given key.
getAdjacentTable() - Method in class org.metaqtl.ChromCluster.ClusterGraph
getAllele(String) - Method in class org.metaqtl.bio.entity.AlleleContainer
getAllele(String) - Method in interface org.metaqtl.bio.IBioLocus
getAlleleNumber() - Method in class org.metaqtl.bio.entity.AlleleContainer
getAlleleNumber() - Method in interface org.metaqtl.bio.IBioLocus
getBestClustering(int) - Method in class org.metaqtl.MetaQtlResult
  This methods returns the best models for each criterion defined to select the optimal number of clusters per trait.
getBestModel(int) - Method in class org.metaqtl.MetaQtlAnalysis
  This methods returns the best models for each criterion defined to select the optimal number of clusters per chromosome per trait.
getBestResult(EMResult[], int) - Static method in class org.metaqtl.EMCriteria
  For the given criterion `criterion` this methods looks into the array of `EMResult` and find the model which is optimal.
getBestResult(EMResult[], int, int) - Static method in class org.metaqtl.EMCriteria
getBestResult(EMResult[], String) - Static method in class org.metaqtl.EMCriteria
getBestResult(EMResult[], int, String) - Static method in class org.metaqtl.EMCriteria
getBioAdapter() - Method in class org.metaqtl.bio.entity.BioEntityCollection
getBioAdapter() - Method in class org.metaqtl.bio.entity.GeneticMap
getBioAdapter() - Method in class org.metaqtl.bio.entity.Individual
getBioAdapter() - Method in class org.metaqtl.bio.entity.LGroup
getBioAdapter() - Method in class org.metaqtl.bio.entity.Marker
getBioAdapter() - Method in class org.metaqtl.bio.entity.Ontology
getBioAdapter() - Method in class org.metaqtl.bio.entity.OntologyTerm
getBioAdapter() - Method in class org.metaqtl.bio.entity.Population
getBioAdapter() - Method in class org.metaqtl.bio.entity.QTL
getBioAdapter() - Method in interface org.metaqtl.bio.IBioAdaptable
getCard() - Method in class org.metaqtl.TreeNode
getCentroid(double[], double[]) - Method in class org.metaqtl.TreeNode
getChildren() - Method in class org.metaqtl.TreeNode
getChildrenTerm() - Method in class org.metaqtl.bio.entity.OntologyTerm
getChildrenTerm() - Method in interface org.metaqtl.bio.IBioOntologyTerm
  Returns the children if the term has chilren, null otherwise.
getChromAxe() - Method in class org.metaqtl.graph.ChromLayer
  Return the axe of the chromosome.
getChromAxe() - Method in class org.metaqtl.graph.ChromShape
getChromAxe() - Method in class org.metaqtl.graph.QtlPartitionLayer
getChromByNames(Chromosome[], String[]) - Static method in class org.metaqtl.main.MetaMain
getChromGraph(Chromosome[], boolean, int, IBioOntology, MetaQtlAnalysis) - Static method in class org.metaqtl.main.MetaMain
getChromIdx(String) - Method in class org.metaqtl.MetaQtlAnalysis
getChromNames() - Method in class org.metaqtl.MetaQtlModel
  Returns the names of the chromosomes.
getChromosomeName(String) - Method in class org.metaqtl.MapCluster
  This method returns the name of the chromosome from the given name.
getChromWidth() - Method in class org.metaqtl.graph.ChromLayer
getChromWidth() - Method in class org.metaqtl.graph.ChromShape
getCluster(String) - Static method in class org.metaqtl.main.MetaMain
getClusterByNames(ChromCluster[], String[]) - Static method in class org.metaqtl.main.MetaMain
getClustering(int) - Method in class org.metaqtl.MetaQtlResult
  Returns the Qtl clustering result with `k` clusters.
getClusterMembers() - Method in class org.metaqtl.ChromCluster
  This method returns the members of the cluster as an array of `Chromosomes`.
getClusters() - Method in class org.metaqtl.MapCluster
  Returns the chromosome clusters.
getCMrkTotalNumbers() - Method in class org.metaqtl.ChromCluster
getCommonMarkerPaths(ChromLayer) - Method in class org.metaqtl.graph.ChromLayer
getCommonMarkerPoints(ChromLayer) - Method in class org.metaqtl.graph.ChromLayer
getCopy() - Method in class org.metaqtl.Qtl
  Returns a copy of the QTL.
getCopy() - Method in class org.metaqtl.Qtl.QTLCross
getCopy() - Method in class org.metaqtl.Qtl.QTLProj
getCopy() - Method in class org.metaqtl.Qtl.QTLStats
getCopy() - Method in class org.metaqtl.Qtl.QTLSupport
getCopy() - Method in class org.metaqtl.Qtl.QTLTrait
getCritDelta(String, int[]) - Method in class org.metaqtl.MetaQtlResult
getCriteria() - Static method in class org.metaqtl.EMCriteria
  Returns an iterator on the criteria
getCriteria() - Method in class org.metaqtl.MetaQtlResult
getCriterion(int) - Method in class org.metaqtl.EMCriteria
  Get the criterion value according to its integer code.
getCriterion(String) - Method in class org.metaqtl.EMCriteria
getCriterion(int) - Method in class org.metaqtl.EMResult
getCriterion() - Method in class org.metaqtl.MetaQtlModel
getCriterionIdx(String) - Static method in class org.metaqtl.EMCriteria
  Returns the integer code for the criterion which matches the given name.
getCritValues(String, int[]) - Method in class org.metaqtl.MetaQtlResult
getCritWeights(String, int[]) - Method in class org.metaqtl.MetaQtlResult
getCrossDesign(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties
  This routine returns an object which handle the properties of the offspring which have been used to create the genetic map.
getCrossType() - Method in class org.metaqtl.bio.entity.CrossPopulation
getCrossType() - Method in interface org.metaqtl.bio.IBioCross
getCSIdx(int, int) - Method in class org.metaqtl.CMarkerSequence
getDataPoints(int, boolean) - Method in class org.metaqtl.MetaQtlData
  For a given trait group indice this methods returns the data points as a matrix of Double X[0..1][0..n-1] where X[0] is the vector of the n position values and X[1] is the vector of the n standard deviations of the positions.
getDF() - Method in interface org.metaqtl.numrec.NumericalUtilities.Function
  Returns the derivative of the function.
getDF() - Method in interface org.metaqtl.numrec.NumericalUtilities.NRFunction
  Returns the value of the derivate in x;
getDico(String) - Static method in class org.metaqtl.main.MetaMain
getDist() - Method in class org.metaqtl.TreeNode
getDistance(int, int, int) - Method in class org.metaqtl.Chromosome
  This methods returns the distance between the first marker and the marker with the given indice using the given mapping context.
getDistance(int) - Method in class org.metaqtl.Chromosome
  This methods returns the distance between the first marker and the marker with the given indice using the default mapping context.
getDistanceBetween(int, int, int, int) - Method in class org.metaqtl.Chromosome
  This methods returns the distance between the markers with the given indices assuming that `mrkIdxL < mrkIdxR`.
getDistanceBetween(int, int) - Method in class org.metaqtl.Chromosome
getDistHeterogeneity(int, int[][], Chromosome, Chromosome) - Static method in class org.metaqtl.Chromosome
getDubious(String) - Static method in class org.metaqtl.main.MetaMain
getEMEps() - Method in class org.metaqtl.algo.QtlClustAlgorithm
getEMRanStartNumber() - Method in class org.metaqtl.algo.QtlClustAlgorithm
getEntity(String) - Method in class org.metaqtl.bio.entity.BioEntityContainer
getEntityBeanClass() - Method in class org.metaqtl.bio.entity.factory.XmlBioEntitiesFactory
getEntityBeanClass() - Method in class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
getEntityBeanClass() - Method in class org.metaqtl.bio.entity.factory.XmlGeneticMapFactory
getEntityBeanClass() - Method in class org.metaqtl.bio.entity.factory.XmlOntologyFactory
getEntityType() - Method in class org.metaqtl.bio.entity.factory.XmlBioEntitiesFactory
getEntityType() - Method in class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
getEntityType() - Method in class org.metaqtl.bio.entity.factory.XmlGeneticMapFactory
getEntityType() - Method in class org.metaqtl.bio.entity.factory.XmlOntologyFactory
getEuclidean() - Method in class org.metaqtl.EMResult
getF() - Method in interface org.metaqtl.numrec.NumericalUtilities.NRFunction
  Returns the value of the function in x.
getFirstCommonMrkIdx(Chromosome, Chromosome) - Static method in class org.metaqtl.Chromosome
getFunction() - Method in class org.metaqtl.bio.entity.Ontology
getFunction() - Method in interface org.metaqtl.bio.IBioOntology
  Returns the function of the ontology
getGeneration() - Method in class org.metaqtl.bio.entity.Population
getGeneration() - Method in interface org.metaqtl.bio.IBioCross
getGenome() - Method in class org.metaqtl.bio.entity.LocusContainer
getGenome() - Method in interface org.metaqtl.bio.IBioLGroup
getGraph() - Method in class org.metaqtl.ChromCluster
getGroup() - Method in class org.metaqtl.bio.entity.AlleleContainer
getGroup(String) - Method in class org.metaqtl.bio.entity.GroupContainer
getGroup() - Method in class org.metaqtl.bio.entity.Locus
getGroup(String) - Method in interface org.metaqtl.bio.IBioGenome
getGroup() - Method in interface org.metaqtl.bio.IBioLocus
getGroups() - Method in class org.metaqtl.bio.entity.bean.GeneticMapBean
getHeight() - Method in class org.metaqtl.graph.ChromAxe
getHeight() - Method in class org.metaqtl.graph.ChromLayer
getHeight() - Method in class org.metaqtl.graph.GraphShape
getHeight() - Method in class org.metaqtl.graph.Layer
getHeight() - Method in class org.metaqtl.graph.MetaGraph
getHeight() - Method in class org.metaqtl.TreeNode
getHeigth() - Method in class org.metaqtl.graph.QtlShape
getID() - Method in class org.metaqtl.bio.entity.OntologyTerm
getID() - Method in interface org.metaqtl.bio.IBioOntologyTerm
  Returns the id if the terms.
getImage(ChromGraph[]) - Static method in class org.metaqtl.graph.GraphFactory
getIndividual(String) - Method in class org.metaqtl.bio.entity.IndividualContainer
getIndividual(String) - Method in interface org.metaqtl.bio.IBioPopulation
getIndividualNumber() - Method in class org.metaqtl.bio.entity.IndividualContainer
getIndividualNumber() - Method in class org.metaqtl.bio.entity.Population
getIndividualNumber() - Method in interface org.metaqtl.bio.IBioPopulation
getInstance() - Static method in class org.metaqtl.bio.util.BioEntityNameComparator
getInstance() - Static method in class org.metaqtl.bio.util.LocusPositionComparator
getK() - Method in class org.metaqtl.EMResult
getKeys() - Method in class org.metaqtl.bio.util.TabulatedReader
  Returns the set of the keys.
getKValues() - Method in class org.metaqtl.MetaQtlResult
getLabelSide() - Method in class org.metaqtl.graph.ChromShape
getLayer(double, double) - Method in class org.metaqtl.graph.QtlLayerBuffer
  Returns a QtlLayer which represent the contents of the buffer.
getLeaf(int) - Method in class org.metaqtl.Tree
getLeafHeights() - Method in class org.metaqtl.Tree
getLeafNumber() - Method in class org.metaqtl.Tree
getLeftCSMarker(int, int) - Method in class org.metaqtl.CMarkerSequence
  Returns the indices of the marker at the left of the given one.
getLocus() - Method in class org.metaqtl.bio.entity.bean.LGroupBean
getLocus(String) - Method in class org.metaqtl.bio.entity.LocusContainer
getLocus() - Method in interface org.metaqtl.bio.IBioAllele
getLocus(String) - Method in interface org.metaqtl.bio.IBioLGroup
getLocusAdapter() - Static method in class org.metaqtl.bio.entity.Locus
getLocusNumber() - Method in class org.metaqtl.bio.entity.LocusContainer
getLocusNumber() - Method in interface org.metaqtl.bio.IBioLGroup
getLocusType() - Method in class org.metaqtl.bio.entity.Marker
getLocusType() - Method in class org.metaqtl.bio.entity.QTL
getLocusType() - Method in interface org.metaqtl.bio.IBioLocus
getLogger() - Method in class org.metaqtl.algo.MetaAlgorithm
  Returns the logger for this algorithm as a `PrintStream`.
getMahalanobis(double[]) - Method in class org.metaqtl.EMResult
getMap(String) - Static method in class org.metaqtl.main.MetaMain
getMap(IBioGenome[], String) - Static method in class org.metaqtl.main.MetaMain
getMapName() - Method in class org.metaqtl.Chromosome
getMappingCross(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties
getMappingFunction(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties
  This methods returns the integer code of the mapping function associated to the given genetic map.
getMappingUnit(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties
getMaps(String) - Static method in class org.metaqtl.main.MetaMain
getMarkerDico() - Method in class org.metaqtl.ChromCluster
getMarkerDico() - Method in class org.metaqtl.MapCluster
getMarkerIdx(int, int, int) - Method in class org.metaqtl.CMarkerSequence
getMarkerIdxWithName(String) - Method in class org.metaqtl.Chromosome
  This method looks if it exists a marker on the chromosome with the given name and returns its indice.
getMarkerIndexByName(String) - Method in class org.metaqtl.ChromCluster
  For a given marker name this method returns the marker index of the marker table if found.
getMarkerIntervalNumber() - Method in class org.metaqtl.ChromCluster
  This method returns the total number of marker intervals, i.e the sum over chromosomes of the number of marker intervals.
getMarkerName(String) - Method in class org.metaqtl.ChromCluster
  This method returns the name of the locus from the given name.
getMarkerName(int) - Method in class org.metaqtl.Chromosome
  Returns the names of the marker at the i^th position on the chromosome.
getMarkerNameByIndex(int) - Method in class org.metaqtl.ChromCluster
  This method returns the name of the marker according to this indice.
getMarkerNumber() - Method in class org.metaqtl.ChromCluster
  This method returns the number of distinct markers implied in this cluster, i.e the size of the marker table.
getMarkerOccurence(int) - Method in class org.metaqtl.ChromCluster
  Returns the number of times the marker with the indice i has been seen over the chromosomes of the cluster.
getMetaOccurence(IBioLocus) - Static method in class org.metaqtl.util.LocusProperties
getMetaQtl(String, String, int) - Method in class org.metaqtl.MetaQtlAnalysis
  Returns the meta Qtl for the given chromosome indice `cidx`, the given trait name `trait` and the given number of clusters `k`.
getMetaQtl(int) - Method in class org.metaqtl.MetaQtlResult
getMetaQtls() - Method in class org.metaqtl.Chromosome
getModel(String, String) - Method in class org.metaqtl.MetaQtlModel
getModel(int, int) - Method in class org.metaqtl.MetaQtlModel
getMrkTickPoint2D(int, boolean) - Method in class org.metaqtl.graph.ChromLayer
getMrkTickPoint2D(int, boolean) - Method in class org.metaqtl.graph.ChromShape
getMrkToRm(File) - Static method in class org.metaqtl.main.MetaMain
getMu(int) - Method in class org.metaqtl.EMResult
getName() - Method in class org.metaqtl.bio.entity.bean.BioEntityBean
getName() - Method in class org.metaqtl.bio.entity.bean.PropertyBean
getName() - Method in class org.metaqtl.bio.entity.BioEntity
getName() - Method in class org.metaqtl.bio.entity.BioEntityCollection
getName() - Method in interface org.metaqtl.bio.IBioEntity
  Returns the name of the biological entity
getName() - Method in class org.metaqtl.ChromCluster
  Returns the name of the cluster.
getName() - Method in class org.metaqtl.Chromosome
  Returns the name of the chromosome.
getName() - Method in class org.metaqtl.Qtl
  Returns the name of the QTL.
getName() - Method in class org.metaqtl.TreeNode
getNodeHeights() - Method in class org.metaqtl.Tree
getNodeNumber() - Method in class org.metaqtl.Tree
getOntology(String, char) - Static method in class org.metaqtl.main.MetaMain
getOption() - Method in exception org.metaqtl.main.CmdLineParser.IllegalOptionValueException
getOptionChar() - Method in exception org.metaqtl.main.CmdLineParser.NotFlagException
getOptionName() - Method in exception org.metaqtl.main.CmdLineParser.UnknownOptionException
getOptionValue(CmdLineParser.Option) - Method in class org.metaqtl.main.CmdLineParser
  Equivalent to `getOptionValue(o, null)`.
getOptionValue(CmdLineParser.Option, Object) - Method in class org.metaqtl.main.CmdLineParser
getOptionValues(CmdLineParser.Option) - Method in class org.metaqtl.main.CmdLineParser
getPalette(int) - Static method in class org.metaqtl.graph.PaletteColor
  Returns a palete of colors which should be distinct.
getPaletteGradient(int, Color, Color) - Static method in class org.metaqtl.graph.PaletteColor
getParent() - Method in class org.metaqtl.bio.entity.BioEntity
getParent() - Method in class org.metaqtl.bio.entity.BioEntityCollection
getParent() - Method in interface org.metaqtl.bio.IBioEntity
  Returns the entity that handles this entity.
getParent() - Method in class org.metaqtl.TreeNode
getParents() - Method in class org.metaqtl.bio.entity.CrossPopulation
getParents() - Method in class org.metaqtl.bio.entity.Individual
getParents() - Method in class org.metaqtl.bio.entity.Population
getParents() - Method in interface org.metaqtl.bio.IBioCross
getParents() - Method in interface org.metaqtl.bio.IBioIndividual
  Returns the pedigree of the individual
getParentTerm() - Method in class org.metaqtl.bio.entity.OntologyTerm
getParentTerm() - Method in interface org.metaqtl.bio.IBioOntologyTerm
  Returns the parent of the term.
getPartNames() - Method in class org.metaqtl.QtlPartition
getPedigree() - Method in class org.metaqtl.bio.entity.Individual
getPi(int) - Method in class org.metaqtl.EMResult
getPopulation() - Method in class org.metaqtl.bio.entity.Individual
getPopulation() - Method in interface org.metaqtl.bio.IBioIndividual
getPosition() - Method in class org.metaqtl.bio.entity.AlleleContainer
getPosition() - Method in class org.metaqtl.bio.entity.Locus
getPosition() - Method in interface org.metaqtl.bio.IBioLocus
getProba() - Method in class org.metaqtl.Chromosome
getProbaColor(double) - Static method in class org.metaqtl.graph.MetaGraphPar
getProbaColor(double, double) - Static method in class org.metaqtl.graph.MetaGraphPar
getProperties() - Method in class org.metaqtl.bio.entity.bean.BioEntityBean
getProperties() - Method in class org.metaqtl.bio.entity.BioEntity
getProperties() - Method in class org.metaqtl.bio.entity.BioEntityCollection
getProperties() - Method in interface org.metaqtl.bio.IBioEntity
  Gets the properties of the entity.
getQtl(int, int) - Method in class org.metaqtl.MetaQtlData
  Returns the j^th QTL in the i^th cluster.
getQtlIdx(int) - Method in class org.metaqtl.MetaQtlData
  Returns the indices of the Qtl for the given trait cluster indice `i`.
getQTLInMrkIntProb(int, int, int) - Method in class org.metaqtl.Chromosome
  This methods returns the probability that the QTL be inside the marker interval with the given right and left marker indices and the given QTL indice.
getQTLInMrkIntProb(int, int, Qtl) - Method in class org.metaqtl.Chromosome
  This methods returns the probability that the QTL be inside the marker interval with the given right and left marker indices and the given QTL.
getQtlNumber() - Method in class org.metaqtl.Chromosome
getQtlNumber() - Method in class org.metaqtl.MetaQtlData
getQtlPartition(Chromosome, IBioOntology) - Static method in class org.metaqtl.main.MetaMain
getQtlPartition(Chromosome, MetaQtlAnalysis, String, int, char) - Static method in class org.metaqtl.main.MetaMain
getQtlPartNames() - Method in class org.metaqtl.graph.QtlPartitionLayer
getQtls() - Method in class org.metaqtl.Chromosome
  This method returns a copy of the QTL located on thic chromosome.
getQTLSD(Qtl.QTLSupport, int, int) - Static method in class org.metaqtl.Qtl
  Depending on the CI type this methods returns the the standard deviation of the QTL position using the given mapping context.
getQTLSD(double, Qtl.QTLCross, int) - Static method in class org.metaqtl.Qtl
  Depending on the r-square parameter and the cross design this method returns the standard deviation of the QTL position for the given mapping context.
getQtlTree() - Method in class org.metaqtl.MetaQtlResult
getRecHeterogeneity(int, int[][], Chromosome, Chromosome) - Static method in class org.metaqtl.Chromosome
getRemainingArgs() - Method in class org.metaqtl.main.CmdLineParser
getResult() - Method in class org.metaqtl.algo.ClustAlgorithm
  When the algorithm is finished use this method to get the result.
getResult() - Method in class org.metaqtl.algo.MetaMapAlgorithm
getResult() - Method in class org.metaqtl.algo.QtlProjAlgorithm
getResult(String) - Static method in class org.metaqtl.main.MetaMain
getResult(String, String) - Method in class org.metaqtl.MetaQtlAnalysis
  Returns the result for the given trait name or null if not found.
getResult(String) - Method in class org.metaqtl.MetaQtlAnalysis
  Returns the first result for the given chromosome.
getResult(int, String) - Method in class org.metaqtl.MetaQtlAnalysis
  Returns the result for the given trait name or null if not found.
getResults(String) - Method in class org.metaqtl.MetaQtlAnalysis
getRightCSMarker(int, int) - Method in class org.metaqtl.CMarkerSequence
getRoot() - Method in class org.metaqtl.bio.entity.Ontology
getRoot() - Method in interface org.metaqtl.bio.IBioOntology
  Returns the root of the ontology tree.
getRoot() - Method in class org.metaqtl.Tree
getSD(int) - Method in class org.metaqtl.EMResult
getSize() - Method in class org.metaqtl.bio.entity.Population
  Returns the size of the population.
getSize() - Method in interface org.metaqtl.bio.IBioCross
getSubChromosome(String[]) - Method in class org.metaqtl.Chromosome
getSuboption() - Method in exception org.metaqtl.main.CmdLineParser.UnknownSuboptionException
getSynonymous(String) - Method in class org.metaqtl.MetaDico
getTerm(IBioOntologyTerm) - Method in class org.metaqtl.bio.entity.Ontology
getTerm(String) - Method in class org.metaqtl.bio.entity.Ontology
getTerm(IBioOntologyTerm) - Method in interface org.metaqtl.bio.IBioOntology
  Returns if exists the term in the ontology which matches the given one.
getTerm(String) - Method in interface org.metaqtl.bio.IBioOntology
  This method looks into the ontology if there is a term with the given name and returns it.
getTerm(String) - Method in class org.metaqtl.MetaDico
getTerms() - Method in class org.metaqtl.MetaDico
getToken() - Method in class org.metaqtl.bio.util.TabulatedReader
getToken() - Method in class org.metaqtl.bio.util.TabulatedWriter
getTraitClusterName(int) - Method in class org.metaqtl.MetaQtlData
getTraitClusterNames() - Method in class org.metaqtl.MetaQtlData
  Returns the names of the trait clusters.
getTraitClusterNumber() - Method in class org.metaqtl.MetaQtlData
  Returns the number of trait groups for this data set as defined by the clustering method.
getTraitClusterSize(int) - Method in class org.metaqtl.MetaQtlData
  Returns the size of the trait cluster i.
getTraitIdx(int, String) - Method in class org.metaqtl.MetaQtlAnalysis
getTraitName() - Method in class org.metaqtl.MetaQtlResult
  Returns the name of the trait cluster for this result.
getTraitNames(String) - Method in class org.metaqtl.MetaQtlModel
getTraitNames(int) - Method in class org.metaqtl.MetaQtlModel
getType() - Method in class org.metaqtl.bio.entity.AlleleContainer
getType() - Method in class org.metaqtl.bio.entity.BioEntity
getType() - Method in class org.metaqtl.bio.entity.BioEntityCollection
getType() - Method in class org.metaqtl.bio.entity.CrossPopulation
getType() - Method in class org.metaqtl.bio.entity.GeneticMap
getType() - Method in class org.metaqtl.bio.entity.GroupContainer
getType() - Method in class org.metaqtl.bio.entity.Individual
getType() - Method in class org.metaqtl.bio.entity.IndividualContainer
getType() - Method in class org.metaqtl.bio.entity.LGroup
getType() - Method in class org.metaqtl.bio.entity.LocusContainer
getType() - Method in class org.metaqtl.bio.entity.Marker
getType() - Method in class org.metaqtl.bio.entity.Ontology
getType() - Method in class org.metaqtl.bio.entity.OntologyTerm
getType() - Method in class org.metaqtl.bio.entity.Population
getType() - Method in class org.metaqtl.bio.entity.QTL
getType() - Method in interface org.metaqtl.bio.IBioEntity
  There are 2 main class of entities.
getType() - Method in interface org.metaqtl.bio.IBioLocus
getType() - Method in class org.metaqtl.bio.util.EstimatedLocusPosition
getType() - Method in interface org.metaqtl.bio.util.ILGroupPosition
getType() - Method in class org.metaqtl.bio.util.LGroupPosition
getType() - Method in class org.metaqtl.bio.util.StaticLocusPosition
getUSD(EMResult, int, int, String) - Method in class org.metaqtl.MetaQtlResult
getValue() - Method in class org.metaqtl.bio.entity.bean.PropertyBean
getValue() - Method in exception org.metaqtl.main.CmdLineParser.IllegalOptionValueException
getValue(String, Locale) - Method in class org.metaqtl.main.CmdLineParser.Option
getVLabels() - Method in class org.metaqtl.ChromCluster.ClusterGraph
getWidth() - Method in class org.metaqtl.graph.ChromLayer
getWidth() - Method in class org.metaqtl.graph.GraphShape
getWidth() - Method in class org.metaqtl.graph.Layer
getWidth() - Method in class org.metaqtl.graph.MetaGraph
getWidth() - Method in class org.metaqtl.graph.QtlShape
getWorkAmount() - Method in class org.metaqtl.algo.MetaAlgorithm
getWorkAmount() - Method in interface org.metaqtl.IMetaAlgorithm
  Returns the amount of the work to do.
getWorkProgress() - Method in class org.metaqtl.algo.MetaAlgorithm
getWorkProgress() - Method in interface org.metaqtl.IMetaAlgorithm
  Returns the amount of work which have already been done.
getX() - Method in class org.metaqtl.graph.AnchoredElement
getX() - Method in class org.metaqtl.graph.ChromAxe
getX() - Method in class org.metaqtl.TreeNode
getXBestPred() - Method in class org.metaqtl.EMResult
getXChrom() - Method in class org.metaqtl.graph.ChromShape
getXPred() - Method in class org.metaqtl.EMResult
getXPredIdx(int) - Method in class org.metaqtl.EMResult
getY() - Method in class org.metaqtl.graph.AnchoredElement
getY() - Method in class org.metaqtl.TreeNode
getYDistance(QtlShape, QtlShape) - Static method in class org.metaqtl.graph.QtlShape
  Computes the distance between two Qtl shapes assuming along the same axe Y (i.e the shapes have same X).
getYMax() - Method in class org.metaqtl.graph.ChromAxe
getYMax() - Method in class org.metaqtl.graph.ChromLayer
getYMax() - Method in class org.metaqtl.graph.ChromShape
getYMax() - Method in class org.metaqtl.graph.GraphShape
getYMax() - Method in class org.metaqtl.graph.Layer
getYMax() - Method in class org.metaqtl.graph.QtlLayer
getYMax() - Method in class org.metaqtl.graph.QtlPartitionLayer
getYMax() - Method in class org.metaqtl.graph.QtlShape
getYMax() - Method in class org.metaqtl.graph.QtlTreeLayer
getYMin() - Method in class org.metaqtl.graph.ChromAxe
getYMin() - Method in class org.metaqtl.graph.ChromLayer
getYMin() - Method in class org.metaqtl.graph.ChromShape
getYMin() - Method in class org.metaqtl.graph.GraphShape
getYMin() - Method in class org.metaqtl.graph.Layer
getYMin() - Method in class org.metaqtl.graph.QtlLayer
getYMin() - Method in class org.metaqtl.graph.QtlPartitionLayer
getYMin() - Method in class org.metaqtl.graph.QtlShape
getYMin() - Method in class org.metaqtl.graph.QtlTreeLayer
getZ(int) - Method in class org.metaqtl.EMResult
GraphFactory - Class in org.metaqtl.graph
GraphFactory() - Constructor for class org.metaqtl.graph.GraphFactory
GraphShape - Class in org.metaqtl.graph
GraphShape() - Constructor for class org.metaqtl.graph.GraphShape
group - Variable in class org.metaqtl.Qtl.QTLTrait
  The name of the group to which the trait belongs.
GroupContainer - Class in org.metaqtl.bio.entity
  Class Description Here
GroupContainer() - Constructor for class org.metaqtl.bio.entity.GroupContainer
GroupContainer(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.GroupContainer
groupNumber() - Method in class org.metaqtl.bio.entity.GroupContainer
groupNumber() - Method in interface org.metaqtl.bio.IBioGenome
groups - Variable in class org.metaqtl.bio.entity.bean.GeneticMapBean
groups() - Method in class org.metaqtl.bio.entity.GroupContainer
groups() - Method in interface org.metaqtl.bio.IBioGenome
gser(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities

## H

hasChildren() - Method in class org.metaqtl.bio.entity.OntologyTerm
hasChildren() - Method in interface org.metaqtl.bio.IBioOntologyTerm
  Returns true if the term has children, false otherwise.
hasNext() - Method in class org.metaqtl.bio.util.TabulatedReader
  Returns true if there is still a line to read.
hasProba() - Method in class org.metaqtl.graph.ChromLayer
hasQTL() - Method in class org.metaqtl.Chromosome
  This method tests if the chromosome have a set of QTL defined.
haveSameFrame(int, int) - Method in class org.metaqtl.CMarkerSequence
HClustAlgorithm - Class in org.metaqtl.algo
  This class implements stantard agglomerative hierarchical clustering methods.
HClustAlgorithm() - Constructor for class org.metaqtl.algo.HClustAlgorithm
HEADER - Static variable in class org.metaqtl.bio.entity.factory.OntologyTabFactory
HEIGHT - Static variable in class org.metaqtl.graph.GraphFactory
height - Variable in class org.metaqtl.graph.GraphShape
height - Variable in class org.metaqtl.graph.Layer
  The height of the layer.
height - Variable in class org.metaqtl.TreeNode
  The distance between the node and the root of the tree (if defined).
help - Variable in class org.metaqtl.main.MetaMain
HORIZONTAL_MODE - Static variable in class org.metaqtl.QtlPartition

## I

IBioAdaptable - Interface in org.metaqtl.bio
IBioAdapter - Interface in org.metaqtl.bio
IBioAllele - Interface in org.metaqtl.bio
  Class Description Here
IBioConstants - Interface in org.metaqtl.bio.entity
  Class Description Here
IBioCross - Interface in org.metaqtl.bio
  Class Description Here
IBioCrossTypes - Interface in org.metaqtl.bio
  Class Description Here
IBioEntity - Interface in org.metaqtl.bio
  Class Description Here
IBioEntityTypes - Interface in org.metaqtl.bio
  Class Description Here
IBioGenome - Interface in org.metaqtl.bio
IBioGenomeProperties - Interface in org.metaqtl
  This interface defines both the keys and the default values of properties which can be handled by a org.thalia.bio.entity.IBioGenome.
IBioIndividual - Interface in org.metaqtl.bio
  Class Description Here
IBioIndividualTree - Interface in org.metaqtl.bio
  Class Description Here
IBioLGroup - Interface in org.metaqtl.bio
IBioLGroupProperties - Interface in org.metaqtl
  This interface defines the key of properties which can be handled by a org.thalia.bio.entity.IBioLGroup.
IBioLocus - Interface in org.metaqtl.bio
IBioLocusProperties - Interface in org.metaqtl
  This interface defines the key of the properties which can be handled by a org.thalia.bio.entity.IBioLocus.
IBioOntology - Interface in org.metaqtl.bio
  This interface defines some rules to handle a ontology.
IBioOntologyTerm - Interface in org.metaqtl.bio
  This class defines a term of an ontology.
IBioPopulation - Interface in org.metaqtl.bio
  Class Description Here
ic1 - Variable in class org.metaqtl.Qtl.QTLSupport
  The recombination rate between the QTL position and the left border of the IC.
ic2 - Variable in class org.metaqtl.Qtl.QTLSupport
  The recombination rate between the QTL position and the right border of the IC.
ICOMP - Static variable in class org.metaqtl.EMCriteria
icomp - Variable in class org.metaqtl.EMCriteria
ICOMP_NAME - Static variable in class org.metaqtl.EMCriteria
id - Variable in class org.metaqtl.bio.entity.bean.OntologyTermBean
  The id of the term.
id - Variable in class org.metaqtl.Qtl
  The id of the Qtl
idx - Variable in class org.metaqtl.TreeNode
  ? The identifiant of the cluster.
idx1 - Variable in class org.metaqtl.CMarkerSequence
  The indices of the markers on the first chromosome for the common sequences.
idx2 - Variable in class org.metaqtl.CMarkerSequence
  The indices of the marker on the second chromosome for the common sequences.
IGeneticMapProperties - Interface in org.metaqtl.bio.entity
  Class Description Here
ILGroupPosition - Interface in org.metaqtl.bio.util
  Class Description Here
IMetaAlgorithm - Interface in org.metaqtl
  This interface defines some methods which are common to data analysis algorithms.
IMetaQtlConstants - Interface in org.metaqtl
  This interface defines some global constants which are used by several classes of the package.
IMIN(int, int) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Returns the min between `a` and `b`
incms - Variable in class org.metaqtl.CMarkerSequence
indexx(int, double[], int[]) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Sort the given array of double arrin[1..n] without destroying it and returns the sorted indices of the array elements into indx[1..n].
Individual - Class in org.metaqtl.bio.entity
  Class Description Here
Individual() - Constructor for class org.metaqtl.bio.entity.Individual
Individual(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.Individual
INDIVIDUAL - Static variable in interface org.metaqtl.bio.IBioEntityTypes
  The integer code for an individual entity
IndividualContainer - Class in org.metaqtl.bio.entity
  Class Description Here
IndividualContainer() - Constructor for class org.metaqtl.bio.entity.IndividualContainer
IndividualContainer(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.IndividualContainer
individuals() - Method in class org.metaqtl.bio.entity.IndividualContainer
individuals() - Method in interface org.metaqtl.bio.IBioPopulation
InfoMap - Class in org.metaqtl.main
InfoMap() - Constructor for class org.metaqtl.main.InfoMap
init(Graphics2D, ChromGraph[]) - Method in class org.metaqtl.graph.MetaGraph
initCmdLineParser() - Method in class org.metaqtl.main.MetaMain
initEM(double[], double[], EMResult, Random) - Static method in class org.metaqtl.algo.EMAlgorithm
  Initializes the EM algorithm by randomly assigning observations to the clusters and do one M-Step to compute the first values of the parameters.
initNodeIdx() - Method in class org.metaqtl.Tree
initPalettes() - Static method in class org.metaqtl.graph.MetaGraphPar
initProbaPalette() - Static method in class org.metaqtl.graph.MetaGraphPar
initQTLPalette() - Static method in class org.metaqtl.graph.MetaGraphPar
initQTLPalette(int) - Static method in class org.metaqtl.graph.MetaGraphPar
initReverse() - Method in class org.metaqtl.Tree
intScale - Variable in class org.metaqtl.Qtl.QTLProj
  The scale ratio between the original flanking marker interval and the one on the map used for projection.
IOntologyTermProperties - Interface in org.metaqtl.bio
IRISe - Static variable in interface org.metaqtl.bio.IBioCrossTypes
IRISi - Static variable in interface org.metaqtl.bio.IBioCrossTypes
isConnected(int) - Method in class org.metaqtl.ChromCluster.ClusterGraph
  Test if the graph is connected
isConnected(int) - Method in class org.metaqtl.ChromCluster
  Tests if the cluster of chromosome is connected using a graph approach.
isDubiousLocus(IBioLocus) - Method in class org.metaqtl.ChromCluster
  If a list of dubious markers has been set before then this routine checks if the given locus is not included into this list.
isDubiousOrderLocus(IBioLocus) - Static method in class org.metaqtl.util.LocusProperties
  Returns true if the given locus has a property order.dubious set to one, false otherwise
isIgnore() - Method in class org.metaqtl.Qtl
  This methods returns true if the QTL must be ignored.
isLoggerEnable() - Method in class org.metaqtl.algo.MetaAlgorithm
ISWAP(int[], int, int) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Swaps elements i and j in a.
iterate(double[], double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  This method performs one iteration of the EM-algorithm.

## K

k - Variable in class org.metaqtl.EMResult
  The number of clusters.

## L

label - Variable in class org.metaqtl.TreeNode
  The label of the cluster
Layer - Class in org.metaqtl.graph
Layer(double, double) - Constructor for class org.metaqtl.graph.Layer
  Creates a layer without any width and heigth constraints which upper left corner will be located at the point (x,y).
LAYER_HSPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
  The horizontal space between layers.
LAYER_VSPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
  The vertical space between layers.
leaf - Variable in class org.metaqtl.TreeNode
  The status of the node.
LEFT_LABEL - Static variable in class org.metaqtl.graph.ChromLayer
LEFT_LABEL - Static variable in class org.metaqtl.graph.ChromShape
LEGEND_BOX_CEX - Static variable in class org.metaqtl.graph.MetaGraphPar
LEGEND_FONT - Static variable in class org.metaqtl.graph.MetaGraphPar
LEGEND_GRAD_HEIGHT - Static variable in class org.metaqtl.graph.MetaGraphPar
LEGEND_GRAD_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
LEGEND_HSPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
LEGEND_PART_HEIGHT - Static variable in class org.metaqtl.graph.MetaGraphPar
LEGEND_PART_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
LEGEND_SCALE_UNIT - Static variable in class org.metaqtl.graph.MetaGraphPar
legendLayer - Variable in class org.metaqtl.graph.MetaGraph
LGroup - Class in org.metaqtl.bio.entity
  Class Description Here
LGroup() - Constructor for class org.metaqtl.bio.entity.LGroup
LGroup(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.LGroup
LGROUP - Static variable in interface org.metaqtl.bio.IBioEntityTypes
  The integer code for Linkage Group entity
LGroupBean - Class in org.metaqtl.bio.entity.bean
  Class Description Here
LGroupBean() - Constructor for class org.metaqtl.bio.entity.bean.LGroupBean
LGroupBeanAdapter - Class in org.metaqtl.bio.entity.adapter
  Class Description Here
LGroupBeanAdapter() - Constructor for class org.metaqtl.bio.entity.adapter.LGroupBeanAdapter
LGroupPosition - Class in org.metaqtl.bio.util
  Class Description Here
LGroupPosition(double) - Constructor for class org.metaqtl.bio.util.LGroupPosition
LGroupPosition(double, double) - Constructor for class org.metaqtl.bio.util.LGroupPosition
load(Reader) - Method in class org.metaqtl.bio.entity.factory.BioEntityFactory
load(InputStream) - Method in class org.metaqtl.bio.entity.factory.BioEntityFactory
load(Reader) - Method in class org.metaqtl.bio.entity.factory.MapChartFactory
  TODO (non-Javadoc)
load(InputStream) - Method in class org.metaqtl.bio.entity.factory.MapChartFactory
  TODO (non-Javadoc)
load(Reader) - Method in class org.metaqtl.bio.entity.factory.MapMakerFactory
load(InputStream) - Method in class org.metaqtl.bio.entity.factory.MapMakerFactory
load(InputStream) - Method in class org.metaqtl.bio.entity.factory.MapRawFactory
load(Reader) - Method in class org.metaqtl.bio.entity.factory.MapRawFactory
load(Reader) - Method in class org.metaqtl.bio.entity.factory.MapTabFactory
load(InputStream) - Method in class org.metaqtl.bio.entity.factory.MapTabFactory
load(InputStream) - Method in class org.metaqtl.bio.entity.factory.OntologyTabFactory
load(Reader) - Method in class org.metaqtl.bio.entity.factory.OntologyTabFactory
  Term_id : the term identifient.
load(InputStream) - Method in class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
load(Reader) - Method in class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
loci() - Method in class org.metaqtl.bio.entity.LocusContainer
loci() - Method in interface org.metaqtl.bio.IBioLGroup
locus - Variable in class org.metaqtl.bio.entity.bean.LGroupBean
Locus - Class in org.metaqtl.bio.entity
Locus() - Constructor for class org.metaqtl.bio.entity.Locus
Locus(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.Locus
LOCUS - Static variable in interface org.metaqtl.bio.IBioEntityTypes
  The integer code for Locus entity
LocusBean - Class in org.metaqtl.bio.entity.bean
  Class Description Here
LocusBean() - Constructor for class org.metaqtl.bio.entity.bean.LocusBean
LocusBeanAdapter - Class in org.metaqtl.bio.entity.adapter
  Class Description Here
LocusBeanAdapter() - Constructor for class org.metaqtl.bio.entity.adapter.LocusBeanAdapter
LocusContainer - Class in org.metaqtl.bio.entity
  Class Description Here
LocusContainer() - Constructor for class org.metaqtl.bio.entity.LocusContainer
LocusContainer(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.LocusContainer
locusNames - Variable in class org.metaqtl.ChromCluster
  Ths locus name index table
LocusPositionComparator - Class in org.metaqtl.bio.util
  Class Description Here
LocusProperties - Class in org.metaqtl.util
LocusProperties() - Constructor for class org.metaqtl.util.LocusProperties
lod - Variable in class org.metaqtl.Qtl.QTLStats
  The lod score of the QTL.
lodDecrease - Variable in class org.metaqtl.Qtl.QTLSupport
  The value of the LOD decrease used to obtain the CI.
logger - Variable in class org.metaqtl.algo.MetaAlgorithm
  The logger.
loggerUp - Variable in class org.metaqtl.algo.MetaAlgorithm
  The logger status.
longForm() - Method in class org.metaqtl.main.CmdLineParser.Option

## M

m - Variable in class org.metaqtl.MultiFitResult
  The number of parameters
m1 - Variable in class org.metaqtl.Qtl
  The indice of the left flanking marker.
m2 - Variable in class org.metaqtl.Qtl
  The indice of the right flanking marker.
main(String[]) - Static method in class org.metaqtl.main.A2Xml
main(String[]) - Static method in class org.metaqtl.main.ConsMap
main(String[]) - Static method in class org.metaqtl.main.InfoMap
main(String[]) - Static method in class org.metaqtl.main.MapView
main(String[]) - Static method in class org.metaqtl.main.MetaDB
main(String[]) - Static method in class org.metaqtl.main.MMapView
main(String[]) - Static method in class org.metaqtl.main.MQTLView
main(String[]) - Static method in class org.metaqtl.main.QTLClust
main(String[]) - Static method in class org.metaqtl.main.QTLClustInfo
main(String[]) - Static method in class org.metaqtl.main.QTLModel
main(String[]) - Static method in class org.metaqtl.main.QTLProj
main(String[]) - Static method in class org.metaqtl.main.QTLTree
main(String[]) - Static method in class org.metaqtl.main.Xml2A
MAKER_NAME_VSPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
manageMissingData(int) - Method in class org.metaqtl.MetaQtlData
  Manage the missing data.
MapChartFactory - Class in org.metaqtl.bio.entity.factory
  General comments must be added here.
MapChartFactory() - Constructor for class org.metaqtl.bio.entity.factory.MapChartFactory
MapCluster - Class in org.metaqtl
MapCluster() - Constructor for class org.metaqtl.MapCluster
  Creates a new instance of `MapCluster`.
MapDBFactory - Class in org.metaqtl.factory
  A factory to read the list and the properties of a set of genetic maps.
MapDBFactory() - Constructor for class org.metaqtl.factory.MapDBFactory
MapMakerFactory - Class in org.metaqtl.bio.entity.factory
MapMakerFactory() - Constructor for class org.metaqtl.bio.entity.factory.MapMakerFactory
mapName - Variable in class org.metaqtl.Chromosome
  The name of the map in which this chromosome is defined.
mapNames - Variable in class org.metaqtl.MetaChrom
  The names of the genetic maps.
mapOrigin - Variable in class org.metaqtl.Qtl.QTLProj
  The name of the map from which this QTL comes.
MAPPING_CROSS - Static variable in interface org.metaqtl.IBioGenomeProperties
  The key for mapping cross.
MAPPING_EXPANSION - Static variable in interface org.metaqtl.IBioGenomeProperties
  The key for mapping expansion status.
MAPPING_FUNCTION - Static variable in interface org.metaqtl.IBioGenomeProperties
  The key for mapping function.
MAPPING_FUNCTION_HALDANE - Static variable in interface org.metaqtl.IBioGenomeProperties
  The code for Haldane mapping function.
MAPPING_FUNCTION_HALDANE - Static variable in interface org.metaqtl.IMetaQtlConstants
  Integer code for haldane mapping function
MAPPING_FUNCTION_KOSAMBI - Static variable in interface org.metaqtl.IBioGenomeProperties
  The code for Kosambi mapping function.
MAPPING_FUNCTION_KOSAMBI - Static variable in interface org.metaqtl.IMetaQtlConstants
  Integer code for kosambi mapping function
MAPPING_FUNCTION_UNKNOWN - Static variable in interface org.metaqtl.IMetaQtlConstants
  Integer code for not defined mapping function
MAPPING_UNIT - Static variable in interface org.metaqtl.IBioGenomeProperties
  The mapping unit key.
MAPPING_UNIT_CM - Static variable in interface org.metaqtl.IBioGenomeProperties
  The code for centi-Morgan unit.
MAPPING_UNIT_CM - Static variable in interface org.metaqtl.IMetaQtlConstants
  Integer code for centi morgan mapping unit
MAPPING_UNIT_M - Static variable in interface org.metaqtl.IBioGenomeProperties
  The code for Morgan unit.
MAPPING_UNIT_M - Static variable in interface org.metaqtl.IMetaQtlConstants
  Integer code for morgan mapping unit
MAPPING_UNIT_UNKNOWN - Static variable in interface org.metaqtl.IMetaQtlConstants
  Integer code for unknown mapping unit
MappingFunction - Class in org.metaqtl.util
  define all cartogarphies functions
MappingFunction() - Constructor for class org.metaqtl.util.MappingFunction
MapRawFactory - Class in org.metaqtl.bio.entity.factory
MapRawFactory() - Constructor for class org.metaqtl.bio.entity.factory.MapRawFactory
mapScale - Variable in class org.metaqtl.Qtl.QTLProj
  The scale ratio between the original map and the map on which the QTL has been projected.
MapTabFactory - Class in org.metaqtl.bio.entity.factory
MapTabFactory() - Constructor for class org.metaqtl.bio.entity.factory.MapTabFactory
MapView - Class in org.metaqtl.main
MapView() - Constructor for class org.metaqtl.main.MapView
mapWeight - Variable in class org.metaqtl.Qtl.QTLProj
  The cumulated scale weights of the common marke sequences between the original map and the map on which the QTL has been projected.
Marker - Class in org.metaqtl.bio.entity
  Class Description Here
Marker() - Constructor for class org.metaqtl.bio.entity.Marker
Marker(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.Marker
MARKER - Static variable in interface org.metaqtl.bio.IBioLocus
MARKER_NAME_FONT - Static variable in class org.metaqtl.graph.MetaGraphPar
MARKER_POSITION_FONT - Static variable in class org.metaqtl.graph.MetaGraphPar
MARKERLOCUS - Static variable in interface org.metaqtl.bio.IBioEntityTypes
mcidx - Variable in class org.metaqtl.CMarkerSequence
  The common marker indices on the chromosomes.
merge(GeneticMap) - Method in class org.metaqtl.bio.entity.GeneticMap
  Deprecated.
mergeGenome(IBioGenome, IBioGenome) - Static method in class org.metaqtl.bio.util.BioUtilities
  This method merges two genomes in a single one : `g1` is modified and will contain the result of the merge.
MetaAlgorithm - Class in org.metaqtl.algo
MetaAlgorithm() - Constructor for class org.metaqtl.algo.MetaAlgorithm
MetaChrom - Class in org.metaqtl
  A MetaChrom is the result of the merge of the members of a `ChromCluster`.
MetaChrom(MultiFitResult, ChromCluster) - Constructor for class org.metaqtl.MetaChrom
  Get a new instance of `MetaChrom` which is initialized by using the result of the merge of the members of a `ChromCluster`.
MetaDB - Class in org.metaqtl.main
MetaDB() - Constructor for class org.metaqtl.main.MetaDB
MetaDico - Class in org.metaqtl
  This class represents a dictionnary of synonyms.
MetaDico() - Constructor for class org.metaqtl.MetaDico
MetaDicoFactory - Class in org.metaqtl.factory
MetaDicoFactory() - Constructor for class org.metaqtl.factory.MetaDicoFactory
MetaGraph - Class in org.metaqtl.graph
MetaGraph() - Constructor for class org.metaqtl.graph.MetaGraph
MetaGraphPar - Class in org.metaqtl.graph
MetaGraphParFactory - Class in org.metaqtl.factory
MetaGraphParFactory() - Constructor for class org.metaqtl.factory.MetaGraphParFactory
MetaMain - Class in org.metaqtl.main
MetaMain() - Constructor for class org.metaqtl.main.MetaMain
MetaMap - Class in org.metaqtl
  A `MetaMap` is a bundle of `MetaChrom` objects.
MetaMap(int) - Constructor for class org.metaqtl.MetaMap
  Creates a new instance of `MetaMap` which will contain `nchr` `MetaChrom` objects.
MetaMapAdapter - Class in org.metaqtl.adapter
  This class defines some usefull methods to adapt `MetaMap` objects into other kinds of objects or the inverse.
MetaMapAdapter() - Constructor for class org.metaqtl.adapter.MetaMapAdapter
MetaMapAlgorithm - Class in org.metaqtl.algo
  This class is dedicated to the construction of a consensus genetic map from a set of genetic maps based on a Weigthed Least Square approach.
MetaMapAlgorithm(IBioGenome[], IBioGenome, IBioLocus[], MetaDico) - Constructor for class org.metaqtl.algo.MetaMapAlgorithm
MetaMapSummaryFactory - Class in org.metaqtl.factory
  A factory to write out the information on a `MetaMap`.
MetaMapSummaryFactory() - Constructor for class org.metaqtl.factory.MetaMapSummaryFactory
metaQtlAnalysis - Variable in class org.metaqtl.Chromosome
  The results of a meta-analysis of QTL.
MetaQtlAnalysis - Class in org.metaqtl
  A QTL meta analysis consists in a clustering of QTL positions over chromosomes for different group of traits.
MetaQtlAnalysis(int) - Constructor for class org.metaqtl.MetaQtlAnalysis
  Creates a new instance of a `MetaQtlAnalysis`
MetaQtlAnalysisAdapter - Class in org.metaqtl.adapter
MetaQtlAnalysisAdapter() - Constructor for class org.metaqtl.adapter.MetaQtlAnalysisAdapter
MetaQtlAnalysisFactory - Class in org.metaqtl.factory
  A factory to deal with the result of a QTL meta-analysis.
MetaQtlAnalysisFactory() - Constructor for class org.metaqtl.factory.MetaQtlAnalysisFactory
MetaQtlAnalysisModelFactory - Class in org.metaqtl.factory
MetaQtlAnalysisModelFactory() - Constructor for class org.metaqtl.factory.MetaQtlAnalysisModelFactory
MetaQtlAnalysisSummaryFactory - Class in org.metaqtl.factory
  A factory to deal with QTL meta-analysis result.
MetaQtlAnalysisSummaryFactory() - Constructor for class org.metaqtl.factory.MetaQtlAnalysisSummaryFactory
MetaQtlData - Class in org.metaqtl
  QTL meta analysis first requires to gather the QTL according to the group trait they belong and then to format the QTL data into data points to perfom clustering.
MetaQtlData(Qtl[]) - Constructor for class org.metaqtl.MetaQtlData
  Create a new instance of `MetaQtlData` which will represent the given array of `Qtl`.
MetaQtlModel - Class in org.metaqtl
MetaQtlModel() - Constructor for class org.metaqtl.MetaQtlModel
MetaQtlModel(int) - Constructor for class org.metaqtl.MetaQtlModel
MetaQtlModelFactory - Class in org.metaqtl.factory
MetaQtlModelFactory() - Constructor for class org.metaqtl.factory.MetaQtlModelFactory
MetaQtlResult - Class in org.metaqtl
  A `MetaQtlResult` is used to store the results of a QTL meta analysis which has been performed for a given trait group on a given chromosome.
MetaQtlResult() - Constructor for class org.metaqtl.MetaQtlResult
MetaQtlResult(String, int) - Constructor for class org.metaqtl.MetaQtlResult
METHOD - Static variable in class org.metaqtl.algo.HClustAlgorithm
  A global variable to control the custering method.
mfc - Variable in class org.metaqtl.Chromosome
  The mapping function for this chromosome
mir - Variable in class org.metaqtl.EMCriteria
missing_sd_mode - Variable in class org.metaqtl.algo.ClustAlgorithm
  This global variable defines the mode of imputation for the QTL for which the standard deviation of the position is not available.
MMapView - Class in org.metaqtl.main
MMapView() - Constructor for class org.metaqtl.main.MMapView
mode - Variable in class org.metaqtl.QtlPartition
  The mode of representation
models - Variable in class org.metaqtl.MetaQtlModel
  The number of Qtl per chromosome and per trait.
mqtls - Variable in class org.metaqtl.Chromosome
  The meta Qtls on this chromosome.
MQTLView - Class in org.metaqtl.main
MQTLView() - Constructor for class org.metaqtl.main.MQTLView
mr - Variable in class org.metaqtl.Chromosome
  The adjacent recombination rate between ordered markers
mrkNames - Variable in class org.metaqtl.Chromosome
  The ordered marker names
mrkNames - Variable in class org.metaqtl.MetaChrom
  The ordered marker names.
mrkOc - Variable in class org.metaqtl.MetaChrom
  The number of occurence per marker oved chromosomes.
mStep(double[], double[], EMResult, double) - Static method in class org.metaqtl.algo.EMAlgorithm
  The Maximization step : here this step is straighforward and simple analytical formula are applied to obtain the new parameter estimates.
mu - Variable in class org.metaqtl.EMResult
  The means of the clusters.
MultiFitResult - Class in org.metaqtl
  This class represents a result of a multilinear regression analysis.
MultiFitResult(int, int) - Constructor for class org.metaqtl.MultiFitResult
  Creates a new instance of `MultiFitResult` with the given number of observations `N` and parameters `M`.
mut - Variable in class org.metaqtl.Chromosome
  The mapping unit for this chromosome

## N

n - Variable in class org.metaqtl.EMResult
  The number of data points.
n - Variable in class org.metaqtl.MultiFitResult
  The number of observations without missing data.
name - Variable in class org.metaqtl.bio.entity.bean.BioEntityBean
name - Variable in class org.metaqtl.bio.entity.bean.PropertyBean
name - Variable in class org.metaqtl.bio.entity.BioEntity
name - Variable in class org.metaqtl.bio.entity.BioEntityCollection
name - Variable in class org.metaqtl.ChromCluster
  The name of the chromosome cluster.
name - Variable in class org.metaqtl.Chromosome
  The name of the chromosome.
name - Variable in class org.metaqtl.graph.QtlUnit
name - Variable in class org.metaqtl.MetaChrom
  The name of the meta chrom.
name - Variable in class org.metaqtl.Qtl
  The name of the QTL.
name - Variable in class org.metaqtl.Qtl.QTLCross
  The name of the cross design.
name - Variable in class org.metaqtl.Qtl.QTLTrait
  The name of the trait.
nc - Variable in class org.metaqtl.MetaChrom
  The number of chromosomes implied.
nchr - Variable in class org.metaqtl.MetaMap
  The number of meta chromosmes.
nchr - Variable in class org.metaqtl.MetaQtlAnalysis
  The number of chromosomes on which the meta-analysis has been performed.
ncs - Variable in class org.metaqtl.CMarkerSequence
  The number of common sequences.
needToBeRescaled(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties
  Returns true if the given map need to be rescaled - due to the mapping extansion for some pedigree designs.
NEG_COMMON - Static variable in class org.metaqtl.graph.ChromLayer
NEG_COMMON_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
newBioEntity(int) - Static method in class org.metaqtl.bio.entity.BioEntity
newCrossPopulation(int, String, IBioEntity) - Static method in class org.metaqtl.bio.entity.Population
newEstimatedLocusPosition(double, double) - Static method in class org.metaqtl.bio.util.LGroupPosition
newLocus(int) - Static method in class org.metaqtl.bio.entity.Locus
  Returns a new Locus from the given locus type.
newLocus(String) - Static method in class org.metaqtl.bio.entity.Locus
  Returns a new Locus from the given locus type.
newStaticLocusPosition(double) - Static method in class org.metaqtl.bio.util.LGroupPosition
nextValues(Hashtable) - Method in class org.metaqtl.bio.util.TabulatedWriter
  Prints one line of tabulated values given the hashtable which links values and keys.
nextValues(String[]) - Method in class org.metaqtl.bio.util.TabulatedWriter
  Print one line of tabulated values by assuming that they are in the same order than the keys.
ni - Variable in class org.metaqtl.ChromCluster
  The total number of marker intervals.
ni - Variable in class org.metaqtl.MetaChrom
  The number of marker intervals implied in this consensus.
nidx - Variable in class org.metaqtl.TreeNode
  The indices of the sub-nodes
nm - Variable in class org.metaqtl.Chromosome
  The number of markers.
nm - Variable in class org.metaqtl.MetaChrom
  The number of markers.
nmc - Variable in class org.metaqtl.ChromCluster
  Total number of common marker between clusters
nmc - Variable in class org.metaqtl.CMarkerSequence
  The number of common marker between chromosomes
nmc - Variable in class org.metaqtl.MetaChrom
  The number of marker per implied chromosome
nmqc - Variable in class org.metaqtl.MetaQtlResult
  The number of meta qtl clusterings.
nodes - Variable in class org.metaqtl.Tree
  The nodes of the tree.
np - Variable in class org.metaqtl.QtlPartition
  The number of partition.
nqtl - Variable in class org.metaqtl.MetaQtlResult
  The number of QTL
nqtl - Variable in class org.metaqtl.QtlPartition
  The number of Qtl.
ntg - Variable in class org.metaqtl.MetaQtlData
  The number of trait group.
ntgQtls - Variable in class org.metaqtl.MetaQtlData
  The number of QTL in each trait group.
NumberFormat - Class in org.metaqtl.bio.util
NumberFormat() - Constructor for class org.metaqtl.bio.util.NumberFormat
NumericalUtilities - Class in org.metaqtl.numrec
  Class Description Here
NumericalUtilities() - Constructor for class org.metaqtl.numrec.NumericalUtilities
NumericalUtilities.Function - Interface in org.metaqtl.numrec
NumericalUtilities.NRFunction - Interface in org.metaqtl.numrec

## O

o_mrkIdxL - Variable in class org.metaqtl.Qtl.QTLProj
  The original indice of the left flanking marker.
o_mrkIdxR - Variable in class org.metaqtl.Qtl.QTLProj
  The original indice of the right flanking marker.
OCCURENCE - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the occurence of markers in a consensus map
ocov - Variable in class org.metaqtl.EMResult
  The observed information (just for means).
OffspringManager - Class in org.metaqtl.util
  Class Description Here
OffspringManager() - Constructor for class org.metaqtl.util.OffspringManager
OffspringManager.HaldaneWaddingtonProportion - Class in org.metaqtl.util
OffspringManager.HaldaneWaddingtonProportion() - Constructor for class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
olog - Variable in class org.metaqtl.EMResult
  The observed loglikelihood.
ontology - Variable in class org.metaqtl.algo.ClustAlgorithm
  The optional trait ontology to use to group Qtl.
Ontology - Class in org.metaqtl.bio.entity
Ontology() - Constructor for class org.metaqtl.bio.entity.Ontology
ONTOLOGY - Static variable in interface org.metaqtl.bio.IBioEntityTypes
ONTOLOGY_TERM - Static variable in interface org.metaqtl.bio.IBioEntityTypes
OntologyBean - Class in org.metaqtl.bio.entity.bean
OntologyBean() - Constructor for class org.metaqtl.bio.entity.bean.OntologyBean
OntologyBeanAdapter - Class in org.metaqtl.bio.entity.adapter
OntologyBeanAdapter() - Constructor for class org.metaqtl.bio.entity.adapter.OntologyBeanAdapter
OntologyTabFactory - Class in org.metaqtl.bio.entity.factory
  A factory to deal with `Ontology`.
OntologyTabFactory() - Constructor for class org.metaqtl.bio.entity.factory.OntologyTabFactory
OntologyTerm - Class in org.metaqtl.bio.entity
OntologyTerm() - Constructor for class org.metaqtl.bio.entity.OntologyTerm
OntologyTermBean - Class in org.metaqtl.bio.entity.bean
OntologyTermBean() - Constructor for class org.metaqtl.bio.entity.bean.OntologyTermBean
OntologyTermBeanAdapter - Class in org.metaqtl.bio.entity.adapter
OntologyTermBeanAdapter() - Constructor for class org.metaqtl.bio.entity.adapter.OntologyTermBeanAdapter
org.metaqtl - package org.metaqtl
org.metaqtl.adapter - package org.metaqtl.adapter
org.metaqtl.algo - package org.metaqtl.algo
org.metaqtl.bio - package org.metaqtl.bio
org.metaqtl.bio.entity - package org.metaqtl.bio.entity
org.metaqtl.bio.entity.adapter - package org.metaqtl.bio.entity.adapter
org.metaqtl.bio.entity.bean - package org.metaqtl.bio.entity.bean
org.metaqtl.bio.entity.factory - package org.metaqtl.bio.entity.factory
org.metaqtl.bio.util - package org.metaqtl.bio.util
org.metaqtl.factory - package org.metaqtl.factory
org.metaqtl.graph - package org.metaqtl.graph
org.metaqtl.main - package org.metaqtl.main
org.metaqtl.numrec - package org.metaqtl.numrec
org.metaqtl.util - package org.metaqtl.util

## P

p1 - Variable in class org.metaqtl.graph.ChromLayer.CMrkTickPoint
p2 - Variable in class org.metaqtl.graph.ChromLayer.CMrkTickPoint
PaletteColor - Class in org.metaqtl.graph
PaletteColor() - Constructor for class org.metaqtl.graph.PaletteColor
parent - Variable in class org.metaqtl.bio.entity.BioEntity
parent - Variable in class org.metaqtl.bio.entity.BioEntityCollection
parent - Variable in class org.metaqtl.TreeNode
  The parent of the node
parents - Variable in class org.metaqtl.bio.entity.Population
parse(String[]) - Method in class org.metaqtl.main.CmdLineParser
  Extract the options and non-option arguments from the given list of command-line arguments.
parse(String[], Locale) - Method in class org.metaqtl.main.CmdLineParser
  Extract the options and non-option arguments from the given list of command-line arguments.
parseChromList(String) - Static method in class org.metaqtl.main.MetaMain
parseCmdLine(String[]) - Method in class org.metaqtl.main.MetaMain
parseCross(String) - Static method in class org.metaqtl.bio.util.BioCrossTypes
  Parse the given string and return if valid the type of cross and the number of generations.
parseDouble(String) - Static method in class org.metaqtl.bio.util.NumberFormat
  This method parse the given string to a double value.
parser - Variable in class org.metaqtl.main.MetaMain
parseType(String) - Static method in class org.metaqtl.bio.util.BioLocusTypes
parseValue(String, Locale) - Method in class org.metaqtl.main.CmdLineParser.Option.DoubleOption
parseValue(String, Locale) - Method in class org.metaqtl.main.CmdLineParser.Option.IntegerOption
parseValue(String, Locale) - Method in class org.metaqtl.main.CmdLineParser.Option.LongOption
parseValue(String, Locale) - Method in class org.metaqtl.main.CmdLineParser.Option
  Override to extract and convert an option value passed on the command-line
parseValue(String, Locale) - Method in class org.metaqtl.main.CmdLineParser.Option.StringOption
partition - Variable in class org.metaqtl.graph.QtlUnit
path - Variable in class org.metaqtl.graph.ChromLayer.CMrkTickPath
pi - Variable in class org.metaqtl.EMResult
  The mixing proportions.
pnames - Variable in class org.metaqtl.QtlPartition
  The partition names.
population - Variable in class org.metaqtl.bio.entity.Individual
Population - Class in org.metaqtl.bio.entity
  Class Description Here
Population() - Constructor for class org.metaqtl.bio.entity.Population
Population(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.Population
POPULATION - Static variable in interface org.metaqtl.bio.IBioEntityTypes
  The integer code for Population entity
pos - Variable in class org.metaqtl.graph.QtlUnit
POS_COMMON - Static variable in class org.metaqtl.graph.ChromLayer
POS_COMMON_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
position - Variable in class org.metaqtl.bio.entity.bean.LocusBean
position - Variable in class org.metaqtl.bio.entity.Locus
position - Variable in class org.metaqtl.Qtl
  The QTL most probable location on the chromosome.
printHelp() - Method in class org.metaqtl.main.A2Xml
printHelp() - Method in class org.metaqtl.main.ConsMap
printHelp() - Method in class org.metaqtl.main.InfoMap
printHelp() - Method in class org.metaqtl.main.MapView
printHelp() - Method in class org.metaqtl.main.MetaDB
printHelp() - Method in class org.metaqtl.main.MetaMain
printHelp() - Method in class org.metaqtl.main.MMapView
printHelp() - Method in class org.metaqtl.main.MQTLView
printHelp() - Method in class org.metaqtl.main.QTLClust
printHelp() - Method in class org.metaqtl.main.QTLClustInfo
printHelp() - Method in class org.metaqtl.main.QTLModel
printHelp() - Method in class org.metaqtl.main.QTLProj
printHelp() - Method in class org.metaqtl.main.QTLTree
printHelp() - Method in class org.metaqtl.main.Xml2A
printImgFormat(int) - Static method in class org.metaqtl.main.MetaMain
printLicense(String, String) - Static method in class org.metaqtl.main.MetaMain
printUsage() - Method in class org.metaqtl.main.A2Xml
printUsage() - Method in class org.metaqtl.main.ConsMap
printUsage() - Method in class org.metaqtl.main.InfoMap
printUsage() - Method in class org.metaqtl.main.MapView
printUsage() - Method in class org.metaqtl.main.MetaDB
printUsage() - Method in class org.metaqtl.main.MetaMain
printUsage() - Method in class org.metaqtl.main.MMapView
printUsage() - Method in class org.metaqtl.main.MQTLView
printUsage() - Method in class org.metaqtl.main.QTLClust
printUsage() - Method in class org.metaqtl.main.QTLClustInfo
printUsage() - Method in class org.metaqtl.main.QTLModel
printUsage() - Method in class org.metaqtl.main.QTLProj
printUsage() - Method in class org.metaqtl.main.QTLTree
printUsage() - Method in class org.metaqtl.main.Xml2A
proba - Variable in class org.metaqtl.Chromosome
  Probabilities defined along the chromosome.
proba - Variable in class org.metaqtl.QtlPartition
  The probabilities of each Qtl to belong to each partition.
PROBA_BIN - Static variable in class org.metaqtl.graph.MetaGraphPar
PROBA_FROM_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
PROBA_PALETTE - Static variable in class org.metaqtl.graph.MetaGraphPar
PROBA_TO_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
proj - Variable in class org.metaqtl.Qtl
  The QTL projection properties.
properties - Variable in class org.metaqtl.bio.entity.bean.BioEntityBean
properties - Variable in class org.metaqtl.bio.entity.BioEntity
properties - Variable in class org.metaqtl.bio.entity.BioEntityCollection
PropertyBean - Class in org.metaqtl.bio.entity.bean
  Class Description Here
PropertyBean() - Constructor for class org.metaqtl.bio.entity.bean.PropertyBean
PropertyBean(String, String) - Constructor for class org.metaqtl.bio.entity.bean.PropertyBean
PVALUE - Static variable in interface org.metaqtl.IBioLGroupProperties
  The key for the p-value.
pvalue - Variable in class org.metaqtl.MetaChrom
  The p-value of this chromosome.
pvalue - Variable in class org.metaqtl.MultiFitResult
  The p-value of the model.
PYTHAG(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Computes sqrt(a^2+b^2)

## Q

QTL - Class in org.metaqtl.bio.entity
  Class Description Here
QTL() - Constructor for class org.metaqtl.bio.entity.QTL
QTL(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.QTL
QTL - Static variable in interface org.metaqtl.bio.IBioLocus
Qtl - Class in org.metaqtl
  A QTL (Quantitative Trait Loci)
Qtl() - Constructor for class org.metaqtl.Qtl
Qtl.QTLCross - Class in org.metaqtl
  This class stores the informations on the cross design used to detect the QTL.
Qtl.QTLCross() - Constructor for class org.metaqtl.Qtl.QTLCross
Qtl.QTLProj - Class in org.metaqtl
  This class stores the QTL projection properties.
Qtl.QTLProj() - Constructor for class org.metaqtl.Qtl.QTLProj
Qtl.QTLStats - Class in org.metaqtl
  This class stores the usual statistics for the QTL.
Qtl.QTLStats() - Constructor for class org.metaqtl.Qtl.QTLStats
Qtl.QTLSupport - Class in org.metaqtl
  This class stores information on the QTL Confidence Interval
Qtl.QTLSupport() - Constructor for class org.metaqtl.Qtl.QTLSupport
Qtl.QTLTrait - Class in org.metaqtl
  This class stores the trait description of a QTL
Qtl.QTLTrait() - Constructor for class org.metaqtl.Qtl.QTLTrait
QTL_CI_FROM - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL confidence interval lower boundary.
QTL_CI_LOD_DECREASE - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL confidence interval LOD decrease.
QTL_CI_TO - Static variable in interface org.metaqtl.IBioLocusProperties
  THe key for the QTL confidence interval upper boundary.
QTL_CI_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
QTL_CI_WIDTH_CEX - Static variable in class org.metaqtl.graph.MetaGraphPar
QTL_CROSS_NAME - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL cross name.
QTL_CROSS_SIZE - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL cross size.
QTL_CROSS_TYPE - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL cross type.
QTL_HSPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
  The horizontal space between Qtl shapes.
QTL_NAME_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
  The color of the QTL names.
QTL_NAME_FONT - Static variable in class org.metaqtl.graph.MetaGraphPar
  The font used for the Qtl names.
QTL_NAME_SPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
QTL_NAME_VSPACE_CEX - Static variable in class org.metaqtl.graph.MetaGraphPar
  The space magnification between the Qtl name and the Qtl confidence interval.
QTL_PALETTE - Static variable in class org.metaqtl.graph.MetaGraphPar
  The color palete for the QTL partition.
QTL_PCH_SIZE - Static variable in class org.metaqtl.graph.MetaGraphPar
QTL_POS_HEIGHT_CEX - Static variable in class org.metaqtl.graph.MetaGraphPar
QTL_POS_WIDTH_CEX - Static variable in class org.metaqtl.graph.MetaGraphPar
QTL_PROB_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
QTL_PROJ_INTSCALE - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL flanking marker interval projection rate.
QTL_PROJ_MAPSCALE - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL confidence interval projection rate.
QTL_PROJ_ORIGIN - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the map of origin of the QTL.
QTL_PROJ_SHAREFLANKING - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL flanking marker interval order preservation.
QTL_PROJ_SWAPFLANKING - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL flanking marker interval reverse order.
QTL_STATS_ADDITIVE - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL additive effect.
QTL_STATS_DOMINANCE - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL dominance effect.
QTL_STATS_RSQUARE - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL rsquare.
QTL_TICK_WIDTH_CEX - Static variable in class org.metaqtl.graph.MetaGraphPar
  The magnification for the tick of the QTL.
QTL_TRAIT_GROUP - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL trait group.
QTL_TRAIT_NAME - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL trait name.
QTL_TRAIT_UNIT - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the QTL trait unit.
QTL_TREE_SCALE - Static variable in class org.metaqtl.graph.MetaGraphPar
QTL_TREE_SPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
QTL_VSPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
  The vertical space between Qtl shapes.
QtlAdapter - Class in org.metaqtl.adapter
  This class defines some usefull methods to adapt `Qtl` object into other kinds of objects or the inverse.
QtlAdapter() - Constructor for class org.metaqtl.adapter.QtlAdapter
qtlByChrom - Variable in class org.metaqtl.MetaQtlAnalysis
  The matrix of qtl by chromosome
qtlCI - Variable in class org.metaqtl.QtlPartition
  The Qtl confidence intervals.
QTLClust - Class in org.metaqtl.main
QTLClust() - Constructor for class org.metaqtl.main.QTLClust
QtlClustAlgorithm - Class in org.metaqtl.algo
  This class defines methods to perform a QTL meta-analysis on a genetic map by applying a clustering of QTL based on a gaussian mixture model and the EM-algorihtm.
QtlClustAlgorithm(IBioGenome, IBioOntology) - Constructor for class org.metaqtl.algo.QtlClustAlgorithm
QtlClustAlgorithm(IBioGenome, String, IBioOntology) - Constructor for class org.metaqtl.algo.QtlClustAlgorithm
QTLClustInfo - Class in org.metaqtl.main
QTLClustInfo() - Constructor for class org.metaqtl.main.QTLClustInfo
qtlIdx - Variable in class org.metaqtl.MetaQtlResult
  The indices of QTL which are implied in the analysis.
QtlLayer - Class in org.metaqtl.graph
QtlLayer(double, double) - Constructor for class org.metaqtl.graph.QtlLayer
QtlLayerBuffer - Class in org.metaqtl.graph
QtlLayerBuffer() - Constructor for class org.metaqtl.graph.QtlLayerBuffer
QTLLOCUS - Static variable in interface org.metaqtl.bio.IBioEntityTypes
QTLModel - Class in org.metaqtl.main
QTLModel() - Constructor for class org.metaqtl.main.QTLModel
qtlNames - Variable in class org.metaqtl.QtlPartition
  The qtl names
qtlPart - Variable in class org.metaqtl.graph.ChromGraph
  The Qtl partition
QtlPartition - Class in org.metaqtl
QtlPartition() - Constructor for class org.metaqtl.QtlPartition
QtlPartitionAdapter - Class in org.metaqtl.adapter
  This class defines some methods to adapt complient objects into a `QtlPartition` object.
QtlPartitionAdapter() - Constructor for class org.metaqtl.adapter.QtlPartitionAdapter
QtlPartitionLayer - Class in org.metaqtl.graph
QtlPartitionLayer(double, double) - Constructor for class org.metaqtl.graph.QtlPartitionLayer
qtlPos - Variable in class org.metaqtl.QtlPartition
  The Qtl positions
QTLProj - Class in org.metaqtl.main
QTLProj() - Constructor for class org.metaqtl.main.QTLProj
QtlProjAlgorithm - Class in org.metaqtl.algo
  This class defines some methods to project QTL positions from a genetic map to another.
QtlProjAlgorithm(IBioGenome[], IBioGenome, IBioLocus[]) - Constructor for class org.metaqtl.algo.QtlProjAlgorithm
  Creates a new instance of `QtlProjAlgorithm` for the given configuration of projection.
qtls - Variable in class org.metaqtl.Chromosome
  The QTLs located on this chromosome.
qtls - Variable in class org.metaqtl.MetaQtlData
  The QTL.
QtlShape - Class in org.metaqtl.graph
QtlShape() - Constructor for class org.metaqtl.graph.QtlShape
qtlShapes - Variable in class org.metaqtl.graph.QtlLayer
  The Qtl shapes.
QTLTree - Class in org.metaqtl.main
QTLTree() - Constructor for class org.metaqtl.main.QTLTree
QtlTreeAlgorithm - Class in org.metaqtl.algo
  This class defines methods to perform agglomerative hierarchical QTL clustering.
QtlTreeAlgorithm(IBioGenome, IBioOntology) - Constructor for class org.metaqtl.algo.QtlTreeAlgorithm
QtlTreeLayer - Class in org.metaqtl.graph
QtlTreeLayer(double, double) - Constructor for class org.metaqtl.graph.QtlTreeLayer
QtlUnit - Class in org.metaqtl.graph
QtlUnit() - Constructor for class org.metaqtl.graph.QtlUnit

## R

r2R() - Method in class org.metaqtl.Chromosome
r2R(int, int) - Method in class org.metaqtl.Chromosome
  Re-scale the chromosome assuming that the distances and recombination fractions are based on the frequency of recombinant genotypes R instead of the real recombination fraction r.
R2r() - Method in class org.metaqtl.Chromosome
R2r(int, int) - Method in class org.metaqtl.Chromosome
  Re-scale the chromosome assuming that the distances and recombination fractions are based on the frequency of recombinant genotypes R instead of the real recombination fraction r.
R2r(double, int, int) - Static method in class org.metaqtl.util.OffspringManager
  This routine returns the recombination rate r for a given value of the propertion of recombibant genotypes R according to the cross design.
r2R(double, int, int) - Static method in class org.metaqtl.util.OffspringManager
  This routine returns the recombination rate r for a given value of the propertion of recombibant genotypes R according to the cross design.
rate - Variable in class org.metaqtl.EMResult
  The quadratric rate of convergence of the algorithm.
read(Reader) - Static method in class org.metaqtl.factory.DubiousLocusFactory
  This routine reads the list of dubious markers from the given file location and returns if succeed an array of `IBioLocus` objects.
read(BufferedReader) - Static method in class org.metaqtl.factory.EMResultFactory
read(Reader) - Static method in class org.metaqtl.factory.MapDBFactory
  This method reads a file formated as follows : map property1 property2 property3 ...
read(Reader) - Static method in class org.metaqtl.factory.MetaDicoFactory
read(InputStream) - Static method in class org.metaqtl.factory.MetaQtlAnalysisFactory
read(Reader) - Static method in class org.metaqtl.factory.MetaQtlAnalysisFactory
read(Reader) - Static method in class org.metaqtl.factory.MetaQtlModelFactory
  This method reads a file formated as follows : Chromosome \t Trait \t Model
read(Reader) - Static method in class org.metaqtl.factory.TreeFactory
read(String) - Static method in class org.metaqtl.factory.TreeFactory
read_newick(Reader) - Static method in class org.metaqtl.factory.TreeFactory
read_newick(String) - Static method in class org.metaqtl.factory.TreeFactory
rebuildPartition(String[]) - Method in class org.metaqtl.QtlPartition
recombination(double, int, int) - Static method in class org.metaqtl.util.MappingFunction
  Returns the recombination rate from the distance.
removeAllele(String) - Method in class org.metaqtl.bio.entity.AlleleContainer
removeAllele(String) - Method in interface org.metaqtl.bio.IBioLocus
removeEntity(String) - Method in class org.metaqtl.bio.entity.BioEntityContainer
removeGroup(String) - Method in class org.metaqtl.bio.entity.GroupContainer
removeGroup(String) - Method in interface org.metaqtl.bio.IBioGenome
removeIndividual(String) - Method in class org.metaqtl.bio.entity.IndividualContainer
removeIndividual(String) - Method in interface org.metaqtl.bio.IBioPopulation
removeLocus(String) - Method in class org.metaqtl.bio.entity.LocusContainer
removeLocus(String) - Method in interface org.metaqtl.bio.IBioLGroup
removeLocus(IBioGenome[], String) - Static method in class org.metaqtl.main.MetaMain
result - Variable in class org.metaqtl.algo.ClustAlgorithm
  The result of the clustering.
resultByChrom - Variable in class org.metaqtl.MetaQtlAnalysis
  The matrix of results where the rows are the chromosomes.
RF - Static variable in interface org.metaqtl.bio.IBioCrossTypes
RIGHT_LABEL - Static variable in class org.metaqtl.graph.ChromLayer
RIGHT_LABEL - Static variable in class org.metaqtl.graph.ChromShape
RILSe - Static variable in interface org.metaqtl.bio.IBioCrossTypes
RILSi - Static variable in interface org.metaqtl.bio.IBioCrossTypes
root - Variable in class org.metaqtl.bio.entity.bean.OntologyBean
  The root of the ontology.
root - Variable in class org.metaqtl.Tree
  The root of the tree.
rsd - Variable in class org.metaqtl.MetaChrom
  The standardized residual between original marker intervals and those of the meta chromosome.
rsd - Variable in class org.metaqtl.MultiFitResult
  The residual standard deviations.
rsquare - Variable in class org.metaqtl.Qtl.QTLStats
  The r-square, i.e the proportion of variance explained by the QTL.
rtsafe(NumericalUtilities.NRFunction, double, double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
run(Chromosome, Chromosome) - Static method in class org.metaqtl.algo.CMSAlgorithm
  This methods find the common marker sequences between the two given chromosomes.
run(double[], double[]) - Static method in class org.metaqtl.algo.HClustAlgorithm
  This method performs a agglomerative clustering of the given data points where `x` is the vector of observed values and `sd` the vector of their standard deviations.
run() - Method in class org.metaqtl.algo.MetaMapAlgorithm
  This method builds a consensus genetic map from the given array of `maps`.
run() - Method in class org.metaqtl.algo.QtlClustAlgorithm
  This method performs a QTL meta-analysis on each chromosome of the given map.
run() - Method in class org.metaqtl.algo.QtlProjAlgorithm
  This routine performs the projection of the QTL from the maps onto the skeleton and returns the chromosomes on which the projection has been done.
run() - Method in class org.metaqtl.algo.QtlTreeAlgorithm
  This method performs an agglomerative hierarchical QTL clustering on each chromosome and returns the result as a `MetaQtlAnalysis` object.
run() - Method in interface org.metaqtl.IMetaAlgorithm
  Run the algorithm.

## S

s_mrkIdxL - Variable in class org.metaqtl.Qtl.QTLProj
  The skeleton indice of the left flanking marker.
s_mrkIdxR - Variable in class org.metaqtl.Qtl.QTLProj
  The skeleton indice of the right flanking marker.
scale(double) - Method in class org.metaqtl.graph.ChromAxe
  Scale the axe in y.
scaleHeight(double) - Method in class org.metaqtl.graph.ChromAxe
scaleY(double) - Method in class org.metaqtl.graph.ChromAxe
sd - Variable in class org.metaqtl.MetaQtlResult
  The QTL position standard deviations.
sd2ci(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
sd_mode - Variable in class org.metaqtl.algo.ClustAlgorithm
  This global variable defines the mode of compuation of the standard deviation of the QTL positions.
sd_mode - Variable in class org.metaqtl.algo.QtlProjAlgorithm
  The mode of compuation of the standard deviation of the QTL positions.
sd_position - Variable in class org.metaqtl.Qtl
  The standard deviation of the QTL position.
sdd - Variable in class org.metaqtl.MetaChrom
  The standard deviation of the position in Morgan.
selfingIndividualInformation(OffspringManager.HaldaneWaddingtonProportion) - Static method in class org.metaqtl.util.OffspringManager
  This routine returns the individual means amount of information for the given generation propertions for a self-fertilization design.
selfingRecurrence(OffspringManager.HaldaneWaddingtonProportion, double) - Static method in class org.metaqtl.util.OffspringManager
  Given the current proportion C,D,E,F and G and the recombination rate r this routine computes the next generation proportions following the recurrence formula of Haldane and Waddington, 1931, Inbreeding and linkage, Genetics 16:357-374 (see section self-fertilization p358).
SEPARATOR - Static variable in class org.metaqtl.factory.MetaQtlModelFactory
set(String, String) - Static method in class org.metaqtl.graph.MetaGraphPar
setCentroid(double) - Method in class org.metaqtl.TreeNode
setChildren(OntologyTerm[]) - Method in class org.metaqtl.bio.entity.OntologyTerm
  Sets the children of the term.
setChromAxe(ChromAxe) - Method in class org.metaqtl.graph.QtlPartitionLayer
setChromAxe(ChromAxe) - Method in class org.metaqtl.graph.QtlTreeLayer
setChromName(int, String) - Method in class org.metaqtl.MetaQtlModel
setCIMiss(int) - Method in class org.metaqtl.algo.ClustAlgorithm
setCIMode(int) - Method in class org.metaqtl.algo.ClustAlgorithm
setClusterings(List) - Method in class org.metaqtl.MetaQtlResult
setClusterings(EMResult[]) - Method in class org.metaqtl.MetaQtlResult
setCriterion(String) - Method in class org.metaqtl.MetaQtlModel
  Set the criterion name which was used to obtain this model
setCrossDesign(IBioGenome, CrossPopulation) - Static method in class org.metaqtl.util.GeneticMapProperties
setCrossType(int) - Method in class org.metaqtl.bio.entity.CrossPopulation
setDF(double) - Method in interface org.metaqtl.numrec.NumericalUtilities.Function
  Sets the derivative of the function at x.
setDubiousMarker(IBioLocus[]) - Method in class org.metaqtl.ChromCluster
  This method sets the list of dubious marker.
setDubiousMarker(IBioLocus[]) - Method in class org.metaqtl.MapCluster
  This method sets the list of dubious marker.
setEMEps(double) - Method in class org.metaqtl.algo.QtlClustAlgorithm
setEMRanStartNumber(int) - Method in class org.metaqtl.algo.QtlClustAlgorithm
setFunction(String) - Method in class org.metaqtl.bio.entity.Ontology
  Set the function of the ontology.
setGeneration(int) - Method in class org.metaqtl.bio.entity.Population
setGenome(IBioGenome) - Method in class org.metaqtl.bio.entity.LocusContainer
setGenome(IBioGenome) - Method in interface org.metaqtl.bio.IBioLGroup
setGroup(IBioLGroup) - Method in class org.metaqtl.bio.entity.AlleleContainer
setGroup(IBioLGroup) - Method in class org.metaqtl.bio.entity.Locus
setGroup(IBioLGroup) - Method in interface org.metaqtl.bio.IBioLocus
setGroups(ArrayList) - Method in class org.metaqtl.bio.entity.bean.GeneticMapBean
setID(long) - Method in class org.metaqtl.bio.entity.OntologyTerm
  Sets the indentifient of the term.
setIgnore(boolean) - Method in class org.metaqtl.Qtl
  Set the status of the QTL.
setKeys(String[]) - Method in class org.metaqtl.bio.util.TabulatedWriter
setLabelSide(int) - Method in class org.metaqtl.graph.ChromLayer
setLabelSide(int) - Method in class org.metaqtl.graph.ChromShape
setLoci(IBioLocus[]) - Method in class org.metaqtl.bio.entity.LocusContainer
setLoci(IBioLocus[]) - Method in interface org.metaqtl.bio.IBioLGroup
setLocus(ArrayList) - Method in class org.metaqtl.bio.entity.bean.LGroupBean
setLocus(IBioLocus) - Method in interface org.metaqtl.bio.IBioAllele
setLogger(Writer) - Method in class org.metaqtl.algo.MetaAlgorithm
setLogger(OutputStream) - Method in class org.metaqtl.algo.MetaAlgorithm
setLogger(Writer) - Method in interface org.metaqtl.IMetaAlgorithm
  Give a `Writer` to the algorithm in order to write out the log info.
setLogger(OutputStream) - Method in interface org.metaqtl.IMetaAlgorithm
  Give a `OutputStream` to the algorithm in order to write out the log info.
setMappingContext(IBioGenome, int, int) - Static method in class org.metaqtl.util.GeneticMapProperties
setMarkerDico(MetaDico) - Method in class org.metaqtl.algo.MetaMapAlgorithm
setMarkerDico(MetaDico) - Method in class org.metaqtl.ChromCluster
setMarkerDico(MetaDico) - Method in class org.metaqtl.MapCluster
setMaxClusterNumber(int) - Method in class org.metaqtl.algo.QtlClustAlgorithm
setMetaQtls(Qtl[]) - Method in class org.metaqtl.Chromosome
setModel(int, int[]) - Method in class org.metaqtl.MetaQtlModel
setMrkThresh(int) - Method in class org.metaqtl.ChromCluster
setMrkThreshold(int) - Method in class org.metaqtl.algo.MetaMapAlgorithm
setName(String) - Method in class org.metaqtl.bio.entity.bean.BioEntityBean
setName(String) - Method in class org.metaqtl.bio.entity.bean.PropertyBean
setName(String) - Method in class org.metaqtl.bio.entity.BioEntity
setName(String) - Method in class org.metaqtl.bio.entity.BioEntityCollection
setName(String) - Method in interface org.metaqtl.bio.IBioEntity
setParameter(String) - Static method in class org.metaqtl.main.MetaMain
setParentTerm(IBioOntologyTerm) - Method in class org.metaqtl.bio.entity.OntologyTerm
  Sets the parent of the term.
setPedigree(IBioIndividualTree) - Method in class org.metaqtl.bio.entity.Individual
setPopulation(IBioPopulation) - Method in class org.metaqtl.bio.entity.Individual
setPopulation(IBioPopulation) - Method in interface org.metaqtl.bio.IBioIndividual
setPosition(ILGroupPosition) - Method in class org.metaqtl.bio.entity.AlleleContainer
setPosition(ILGroupPosition) - Method in class org.metaqtl.bio.entity.Locus
setPosition(double) - Method in class org.metaqtl.bio.entity.Locus
  Set the position of the locus on the linkage group in static mode i.e without uncertainty.
setPosition(double, double) - Method in class org.metaqtl.bio.entity.Locus
  Set the position of the locus on the linkage group in estimate mode i.e with uncertainty.
setPosition(ILGroupPosition) - Method in interface org.metaqtl.bio.IBioLocus
setPosition(double) - Method in interface org.metaqtl.bio.IBioLocus
setPosition(double, double) - Method in interface org.metaqtl.bio.IBioLocus
setProba(double[][]) - Method in class org.metaqtl.Chromosome
setProperties(ArrayList) - Method in class org.metaqtl.bio.entity.bean.BioEntityBean
setProperties(Properties) - Method in class org.metaqtl.bio.entity.BioEntity
setProperties(Properties) - Method in class org.metaqtl.bio.entity.BioEntityCollection
setProperties(Properties) - Method in interface org.metaqtl.bio.IBioEntity
  Sets the properties of the entity.
setPvalue(double) - Method in class org.metaqtl.algo.QtlProjAlgorithm
setQtlIdx(int[]) - Method in class org.metaqtl.MetaQtlResult
  Set the indices of the Qtl which are implied in this result.
setRatio(double) - Method in class org.metaqtl.algo.QtlProjAlgorithm
setRoot(IBioOntologyTerm) - Method in class org.metaqtl.bio.entity.Ontology
setRoot(OntologyTerm) - Method in class org.metaqtl.bio.entity.Ontology
setRoot(IBioOntologyTerm) - Method in interface org.metaqtl.bio.IBioOntology
  Sets the root of the ontology.
setSD(Double[]) - Method in class org.metaqtl.MetaQtlResult
  Set the standard deviations of the Qtl.
setSize(int) - Method in class org.metaqtl.bio.entity.Population
  Set the population size.
setTerm(String, List) - Method in class org.metaqtl.MetaDico
setToken(String) - Method in class org.metaqtl.bio.util.TabulatedReader
setToken(String) - Method in class org.metaqtl.bio.util.TabulatedWriter
setTraitNames(int, String[]) - Method in class org.metaqtl.MetaQtlModel
setTree(Tree) - Method in class org.metaqtl.MetaQtlResult
setTree(Tree) - Method in class org.metaqtl.QtlPartition
setTreeMethod(int) - Method in class org.metaqtl.algo.QtlTreeAlgorithm
setValue(String) - Method in class org.metaqtl.bio.entity.bean.PropertyBean
setX(double) - Method in class org.metaqtl.graph.AnchoredElement
setX(double) - Method in class org.metaqtl.graph.ChromAxe
setX(Double[]) - Method in class org.metaqtl.MetaQtlResult
  Set the observed positions of the Qtl.
setX(double) - Method in class org.metaqtl.TreeNode
setY(double) - Method in class org.metaqtl.graph.AnchoredElement
setY(double) - Method in class org.metaqtl.TreeNode
setYMax(double) - Method in class org.metaqtl.graph.ChromAxe
setYMin(double) - Method in class org.metaqtl.graph.ChromAxe
SF - Static variable in interface org.metaqtl.bio.IBioCrossTypes
shareFlanking - Variable in class org.metaqtl.Qtl.QTLProj
  True if the two maps share a common marker sequence around the QTL.
shortForm() - Method in class org.metaqtl.main.CmdLineParser.Option
SIGN(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Returns abs(a) if b > 0, -abs(a) otherwise.
SINGLE_COMMON - Static variable in class org.metaqtl.graph.ChromLayer
SINGLE_COMMON_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
size - Variable in class org.metaqtl.bio.entity.Population
size() - Method in class org.metaqtl.bio.util.TabulatedReader
  Returns the number of keys, i.e the number of columns in the file.
size() - Method in class org.metaqtl.bio.util.TabulatedWriter
size - Variable in class org.metaqtl.Qtl.QTLCross
  The number of individuals.
skeleton - Variable in class org.metaqtl.Chromosome
  The skeleton status for this member
sortCluster() - Method in class org.metaqtl.EMResult
  Sort the components in increasing order.
sortLociByPosition(IBioLocus[]) - Static method in class org.metaqtl.bio.util.BioUtilities
  Sort tab with loci
SQR(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Returns a^2
standardError() - Method in interface org.metaqtl.bio.util.ILGroupPosition
standardError() - Method in class org.metaqtl.bio.util.LGroupPosition
STATIC - Static variable in interface org.metaqtl.bio.util.ILGroupPosition
StaticLocusPosition - Class in org.metaqtl.bio.util
  Class Description Here
StaticLocusPosition(double) - Constructor for class org.metaqtl.bio.util.StaticLocusPosition
stats - Variable in class org.metaqtl.Qtl
  The QTL statistics
status - Variable in class org.metaqtl.graph.ChromLayer.CMrkTickPath
status - Variable in class org.metaqtl.graph.ChromLayer.CMrkTickPoint
stderr - Variable in class org.metaqtl.bio.entity.bean.LocusBean
stderr - Variable in class org.metaqtl.bio.util.LGroupPosition
string2color(String) - Static method in class org.metaqtl.graph.MetaGraphPar
string2font(String) - Static method in class org.metaqtl.graph.MetaGraphPar
summarize(OutputStream) - Method in class org.metaqtl.ChromCluster.ClusterGraph
SVDAlgorithm - Class in org.metaqtl.algo
  This class defines methods to solve usual linear algebra problems by using Singular Value Decomposition (SVD) strategy.
SVDAlgorithm() - Constructor for class org.metaqtl.algo.SVDAlgorithm
SVDBackSub(double[][], double[], double[][], double[], int, int) - Static method in class org.metaqtl.algo.SVDAlgorithm
  Solves A.X=B for a vector X, where `A` is specified by the matrix `U`,`V` and the vector `w` as returned by the SVDecomposition() method.
SVDecomposition(double[][], double[][], double[], int, int) - Static method in class org.metaqtl.algo.SVDAlgorithm
  Given a matrix `A`, this routine computes its singular value decomposition A = U.W.V' .
SVDMFit(double[][], double[], double[], int, int) - Static method in class org.metaqtl.algo.SVDAlgorithm
  Given a set of data points y[1..m] with indiviudal weights w[1..m], use chi2 minimization to determine the coefficients a[1..n] of the fitting function y = X*a.
swap - Variable in class org.metaqtl.Qtl.QTLProj
  True if the flanking marker order are inversed between the skeleton and the original map.
synchChromGraphs(ChromGraph[], Set) - Static method in class org.metaqtl.main.MetaMain
SYNONYMS - Static variable in interface org.metaqtl.bio.IOntologyTermProperties
  The synonyms property for a term in a ontology.

## T

TabulatedReader - Class in org.metaqtl.bio.util
  This class can be used to parse tabulated file in which the first line contains the label of the tabulated fields.
TabulatedReader(Reader) - Constructor for class org.metaqtl.bio.util.TabulatedReader
TabulatedReader(InputStream) - Constructor for class org.metaqtl.bio.util.TabulatedReader
TabulatedWriter - Class in org.metaqtl.bio.util
  General comments must be added here.
TabulatedWriter(OutputStream) - Constructor for class org.metaqtl.bio.util.TabulatedWriter
TabulatedWriter(Writer) - Constructor for class org.metaqtl.bio.util.TabulatedWriter
TEXT_WIDTH - Static variable in class org.metaqtl.graph.QtlLayer
  The default width of the Text attribute of the Qtl
tgidx - Variable in class org.metaqtl.MetaQtlData
  The indices of the QTL in the trait groups.
tgnames - Variable in class org.metaqtl.MetaQtlData
  The trait group names.
theta - Variable in class org.metaqtl.MultiFitResult
  The parameter estimates.
TICK_CEX_HEIGHT - Static variable in class org.metaqtl.graph.QtlLayer
  The default cex parameter for the tick height of the Qtl
TICK_CEX_WIDTH - Static variable in class org.metaqtl.graph.QtlLayer
  The default cex parameter for the tick width of the Qtl
TINY_MAPPING_DISTANCE - Static variable in interface org.metaqtl.IMetaQtlConstants
  The minimal distance in morgan
TINY_MAPPING_VARIANCE - Static variable in interface org.metaqtl.IMetaQtlConstants
  the minimal variance in morgan
TINY_Z_PROBA - Static variable in class org.metaqtl.algo.EMAlgorithm
  The minimal value for Z proba in EM-clustering
to - Variable in class org.metaqtl.graph.QtlUnit
to - Variable in class org.metaqtl.Qtl.QTLSupport
  The position from the first marker to the right border of the IC.
toChromosome(IBioLGroup, IBioCross, int, int) - Static method in class org.metaqtl.adapter.ChromosomeAdapter
  This method converts a linkage group into a chromosome of type `Chromosome` with the given cross design and the given mapping context.
toChromosomes(IBioGenome) - Static method in class org.metaqtl.adapter.ChromosomeAdapter
  This methods converts the given map into an array of `Chromosome` which represents the chromosomes of the input mpe.
toEntity(BioEntityBean, IBioEntity) - Static method in class org.metaqtl.bio.entity.adapter.BioEntityAdapter
toEntity(Object) - Method in class org.metaqtl.bio.entity.adapter.BioEntityCollectionAdapter
toEntity(Object) - Method in class org.metaqtl.bio.entity.adapter.GeneticMapBeanAdapter
toEntity(Object) - Method in class org.metaqtl.bio.entity.adapter.LGroupBeanAdapter
toEntity(Object) - Method in class org.metaqtl.bio.entity.adapter.LocusBeanAdapter
toEntity(Object) - Method in class org.metaqtl.bio.entity.adapter.OntologyBeanAdapter
toEntity(Object) - Method in class org.metaqtl.bio.entity.adapter.OntologyTermBeanAdapter
toEntity(Object) - Method in interface org.metaqtl.bio.IBioAdapter
  Convert the given bio entity object into another compliant object.
toIBioGenome(Chromosome[], int) - Static method in class org.metaqtl.adapter.ChromosomeAdapter
  This routine converts an array of chromosomes into a genetic map with as many chromosomes as the length of the array.
toIBioGenome(MetaMap) - Static method in class org.metaqtl.adapter.MetaMapAdapter
  This methos convert a `MetaMap` object into an object which is consistent with the `IBioGenome` interface.
toQTL(IBioLocus) - Static method in class org.metaqtl.adapter.QtlAdapter
  This method converts an object which class implements the `IBioLocus`interface into a `Qtl`.``
toString() - Method in class org.metaqtl.bio.entity.LGroup
toString() - Method in class org.metaqtl.Chromosome
toString() - Method in class org.metaqtl.MultiFitResult
totd - Variable in class org.metaqtl.Chromosome
  The total distance of the chromosome.
trait - Variable in class org.metaqtl.MetaQtlResult
  The name of the trait.
trait - Variable in class org.metaqtl.Qtl
  The QTL trait data.
traitNames - Variable in class org.metaqtl.MetaQtlModel
  The trait names per chromosome.
transformY(double) - Method in class org.metaqtl.graph.ChromAxe
  Do a affine transformation of the given position `d` which is assumed to be in [0,dmax] in order to have its representation in the chromosome axe.
tree - Variable in class org.metaqtl.MetaQtlResult
  The qtl tree
tree - Variable in class org.metaqtl.QtlPartition
  The Qtl tree.
Tree - Class in org.metaqtl
  This class defines a tree.
Tree() - Constructor for class org.metaqtl.Tree
Tree(TreeNode) - Constructor for class org.metaqtl.Tree
tree_method - Variable in class org.metaqtl.algo.QtlTreeAlgorithm
  This global variable defines the method used by the aglomerative hierarchical clustering.
TREE_NODE_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
TreeFactory - Class in org.metaqtl.factory
  A factory to deal with distance trees.
TreeFactory() - Constructor for class org.metaqtl.factory.TreeFactory
TreeNode - Class in org.metaqtl
  This class represents a node in a binary Tree obtained when applying usual hirarchical clustering methods.
TreeNode(int) - Constructor for class org.metaqtl.TreeNode
  Creates a new instance of `TreeNode` with the given indice `idx`.
TreeNode(int, TreeNode[]) - Constructor for class org.metaqtl.TreeNode
  Creates a new instance of `TreeNode` with the given indice `idx` and the children of the node.
TreeNode() - Constructor for class org.metaqtl.TreeNode
  Creates a new instance of `TreeNode` with default attribute values.
type - Variable in class org.metaqtl.bio.entity.bean.LocusBean
type - Static variable in class org.metaqtl.bio.util.BioCrossTypes
type - Variable in class org.metaqtl.Qtl.QTLCross
  The type of the cross.
TypesString - Static variable in interface org.metaqtl.bio.IBioLocus
typeToString(int) - Static method in class org.metaqtl.bio.util.BioLocusTypes

## U

unit - Variable in class org.metaqtl.Qtl.QTLTrait
  The unit of the trait.
UNKNOWN - Static variable in interface org.metaqtl.bio.IBioCrossTypes
unload(IBioEntity, Writer) - Method in class org.metaqtl.bio.entity.factory.BioEntityFactory
unload(IBioEntity, OutputStream) - Method in class org.metaqtl.bio.entity.factory.BioEntityFactory
unload(IBioEntity, Writer) - Method in class org.metaqtl.bio.entity.factory.MapChartFactory
  TODO (non-Javadoc)
unload(IBioEntity, OutputStream) - Method in class org.metaqtl.bio.entity.factory.MapChartFactory
  TODO (non-Javadoc)
unload(IBioEntity, Writer) - Method in class org.metaqtl.bio.entity.factory.MapMakerFactory
unload(IBioEntity, OutputStream) - Method in class org.metaqtl.bio.entity.factory.MapMakerFactory
unload(IBioEntity, Writer) - Method in class org.metaqtl.bio.entity.factory.MapRawFactory
unload(IBioEntity, OutputStream) - Method in class org.metaqtl.bio.entity.factory.MapRawFactory
unload(IBioEntity, Writer) - Method in class org.metaqtl.bio.entity.factory.MapTabFactory
unload(IBioEntity, OutputStream) - Method in class org.metaqtl.bio.entity.factory.MapTabFactory
unload(IBioEntity, Writer) - Method in class org.metaqtl.bio.entity.factory.OntologyTabFactory
unload(IBioEntity, OutputStream) - Method in class org.metaqtl.bio.entity.factory.OntologyTabFactory
unload(IBioEntity, OutputStream) - Method in class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
unload(IBioEntity, Writer) - Method in class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
update(Reader) - Static method in class org.metaqtl.factory.MetaGraphParFactory
updateLeafIdx(int[]) - Method in class org.metaqtl.Tree
updateLoglikelihood(double[], double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  Updates the loglikelihood value.
updateMappingContext(int, int) - Method in class org.metaqtl.Chromosome
  Updates the mapping context of the chromosome.
updateMuVector(double[], double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  Updates the vector of mixture components and returns the new values.
updatePiVector(EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  Updates the vector of mixture mixings and returns the new values.
updateZMatrix(double[], double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  Updates the Z matrix.

## V

value - Variable in class org.metaqtl.bio.entity.bean.PropertyBean
varianceDistance(double, double, int, int) - Static method in class org.metaqtl.util.MappingFunction
  Returns the variance of the distance for a given recombination rate r, its variance and the mapping function.
verbose - Variable in class org.metaqtl.main.MetaMain
VERSION - Static variable in interface org.metaqtl.IMetaQtlConstants
  The version of the package.
VERTICAL_MODE - Static variable in class org.metaqtl.QtlPartition
virtual - Variable in class org.metaqtl.bio.entity.bean.OntologyTermBean
  The virual status of the term.

## W

wantsValue() - Method in class org.metaqtl.main.CmdLineParser.Option
  Tells whether or not this option wants a value
WARD_METHOD - Static variable in class org.metaqtl.algo.HClustAlgorithm
  Ward method
WardMethod(double[], double[]) - Static method in class org.metaqtl.algo.HClustAlgorithm
  This method performs a hierarchical clustering of the given data points using the Ward's method.
WIDTH - Static variable in class org.metaqtl.graph.GraphFactory
width - Variable in class org.metaqtl.graph.GraphShape
width - Variable in class org.metaqtl.graph.Layer
  The width of the layer.
width - Variable in class org.metaqtl.graph.QtlUnit
WITH_CHROM_NAME - Static variable in class org.metaqtl.graph.MetaGraphPar
WITH_COMMON_MARKER - Static variable in class org.metaqtl.graph.MetaGraphPar
WITH_LEGEND - Static variable in class org.metaqtl.graph.MetaGraphPar
WITH_MAP_NAME - Static variable in class org.metaqtl.graph.MetaGraphPar
WITH_MARKER_NAME - Static variable in class org.metaqtl.graph.MetaGraphPar
WITH_MARKER_POSITION - Static variable in class org.metaqtl.graph.MetaGraphPar
WITH_QTL_NAME - Static variable in class org.metaqtl.graph.MetaGraphPar
  Add the Qtl name.
workAmount - Variable in class org.metaqtl.algo.MetaAlgorithm
  The amount of work to do.
workProgress - Variable in class org.metaqtl.algo.MetaAlgorithm
  The amount of work done.
write(EMResult, OutputStream) - Static method in class org.metaqtl.factory.EMResultFactory
write(EMResult, PrintWriter) - Static method in class org.metaqtl.factory.EMResultFactory
write(OutputStream) - Static method in class org.metaqtl.factory.MetaGraphParFactory
write(Writer) - Static method in class org.metaqtl.factory.MetaGraphParFactory
write(MetaMap, OutputStream) - Static method in class org.metaqtl.factory.MetaMapSummaryFactory
  This methods writes out the summary for a consensus genetic map into a given output stream `stream`.
write(MetaQtlAnalysis, OutputStream) - Static method in class org.metaqtl.factory.MetaQtlAnalysisFactory
  This methods writes out in the given `stream` the results of a QTL meta-analysis.
write(MetaQtlAnalysis, OutputStream) - Static method in class org.metaqtl.factory.MetaQtlAnalysisModelFactory
write(MetaQtlAnalysis, Writer) - Static method in class org.metaqtl.factory.MetaQtlAnalysisModelFactory
write(MetaQtlAnalysis, OutputStream) - Static method in class org.metaqtl.factory.MetaQtlAnalysisSummaryFactory
  This method writes out the summary for a givene QTL meta-analysis result `analysis` on the given output stream `stream`.
write(MetaQtlModel, OutputStream) - Static method in class org.metaqtl.factory.MetaQtlModelFactory
write(MetaQtlModel, Writer) - Static method in class org.metaqtl.factory.MetaQtlModelFactory
write(Tree, OutputStream) - Static method in class org.metaqtl.factory.TreeFactory
  This method writes out the given tree `nodes` as an array of `TreeNode` on the given output stream stream.
write(Tree, PrintWriter) - Static method in class org.metaqtl.factory.TreeFactory
  This method writes out the given tree `nodes` as an array of `TreeNode` using the given writer writer.
writeImg(ChromGraph[], File, String) - Static method in class org.metaqtl.main.MetaMain
writeMap(IBioGenome, String, String) - Static method in class org.metaqtl.main.MetaMain
writeMap(IBioGenome, String) - Static method in class org.metaqtl.main.MetaMain
writePar(File) - Static method in class org.metaqtl.main.MetaMain

## X

x - Variable in class org.metaqtl.graph.AnchoredElement
x - Variable in class org.metaqtl.graph.GraphShape
x - Variable in class org.metaqtl.graph.QtlUnit
x - Variable in class org.metaqtl.MetaQtlResult
  The QTL positions.
x - Variable in class org.metaqtl.TreeNode
xc - Variable in class org.metaqtl.TreeNode
Xml2A - Class in org.metaqtl.main
Xml2A() - Constructor for class org.metaqtl.main.Xml2A
XmlBioEntitiesFactory - Class in org.metaqtl.bio.entity.factory
  Class Description Here
XmlBioEntitiesFactory() - Constructor for class org.metaqtl.bio.entity.factory.XmlBioEntitiesFactory
XmlBioEntityFactory - Class in org.metaqtl.bio.entity.factory
  Class Description Here
XmlBioEntityFactory() - Constructor for class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
XmlGeneticMapFactory - Class in org.metaqtl.bio.entity.factory
  Class Description Here
XmlGeneticMapFactory() - Constructor for class org.metaqtl.bio.entity.factory.XmlGeneticMapFactory
XmlOntologyFactory - Class in org.metaqtl.bio.entity.factory
XmlOntologyFactory() - Constructor for class org.metaqtl.bio.entity.factory.XmlOntologyFactory

## Y

y - Variable in class org.metaqtl.graph.AnchoredElement
y - Variable in class org.metaqtl.graph.GraphShape
y - Variable in class org.metaqtl.TreeNode
y_from - Variable in class org.metaqtl.graph.QtlShape
y_pos - Variable in class org.metaqtl.graph.QtlShape

## Z

z - Variable in class org.metaqtl.EMResult
  The cluster membership probabilties.

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